Experiment: 9RWY

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9HXT

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	pH 8.5 0.12 M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine); 0.1 M Imidazole/MES; 30.00% v/v PEG 500 MME; 30.00% v/v PEG 20K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.86

Symmetry
Space Group	P 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2023-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	82.52	90.7	0.132	0.186	0.132	0.99	5	3.8		310143

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98			1.204	1.702	1.204	0.392		3.9

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.95	79.934	309285	15615	90.47	0.258	0.256	0.2606	0.2954	0.2994	37.439

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.634	0.557	0.111	-0.885	-2.008	2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.716
r_dihedral_angle_3_deg	15.346
r_dihedral_angle_2_deg	11.323
r_dihedral_angle_1_deg	7.319
r_lrange_it	6.439
r_lrange_other	6.439
r_scangle_it	4.753
r_scangle_other	4.753
r_mcangle_it	4.38
r_mcangle_other	4.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.716
r_dihedral_angle_3_deg	15.346
r_dihedral_angle_2_deg	11.323
r_dihedral_angle_1_deg	7.319
r_lrange_it	6.439
r_lrange_other	6.439
r_scangle_it	4.753
r_scangle_other	4.753
r_mcangle_it	4.38
r_mcangle_other	4.38
r_scbond_it	3.273
r_scbond_other	3.273
r_mcbond_it	3.11
r_mcbond_other	3.11
r_dihedral_angle_other_2_deg	1.979
r_angle_refined_deg	1.821
r_angle_other_deg	0.638
r_nbd_other	0.351
r_symmetry_xyhbond_nbd_refined	0.327
r_symmetry_nbd_refined	0.32
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_other	0.113
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.076
r_ncsr_local_group_5	0.062
r_ncsr_local_group_6	0.061
r_ncsr_local_group_12	0.06
r_ncsr_local_group_1	0.059
r_ncsr_local_group_7	0.058
r_ncsr_local_group_27	0.058
r_ncsr_local_group_13	0.057
r_ncsr_local_group_16	0.057
r_ncsr_local_group_17	0.057
r_ncsr_local_group_20	0.057
r_ncsr_local_group_3	0.056
r_ncsr_local_group_4	0.056
r_ncsr_local_group_10	0.056
r_ncsr_local_group_26	0.056
r_ncsr_local_group_15	0.055
r_ncsr_local_group_21	0.055
r_ncsr_local_group_28	0.055
r_ncsr_local_group_9	0.054
r_ncsr_local_group_18	0.054
r_ncsr_local_group_8	0.053
r_ncsr_local_group_25	0.053
r_ncsr_local_group_2	0.052
r_ncsr_local_group_11	0.052
r_ncsr_local_group_22	0.052
r_ncsr_local_group_23	0.051
r_ncsr_local_group_19	0.05
r_ncsr_local_group_24	0.05
r_ncsr_local_group_14	0.046
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32575
Nucleic Acid Atoms
Solvent Atoms	2237
Heterogen Atoms	468

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9RWY | pdb_00009rwy