9H8W | pdb_00009h8w

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9H6O

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.15 M DL-Malic acid 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.65

Symmetry
Space Group	P 21 21 21

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 EIGER2 XE 16M		2022-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97499	Diamond	I04

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	2	48.37	100	0.199	0.201	0.027	0.999	11.5	54		53201

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	2	2.03	100		2.082	2.103	0.291	0.875	0.6	51.5

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	2	48.369	53114	2682	99.889	0.218	0.2156	0.2188	0.2738	0.2754	48.305

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]
4.69			-0.376		-4.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.543
r_dihedral_angle_3_deg	13.764
r_dihedral_angle_2_deg	9.888
r_lrange_it	8.246
r_lrange_other	8.246
r_dihedral_angle_1_deg	7.626
r_scangle_it	6.744
r_scangle_other	6.744
r_mcangle_it	6.23
r_mcangle_other	6.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.543
r_dihedral_angle_3_deg	13.764
r_dihedral_angle_2_deg	9.888
r_lrange_it	8.246
r_lrange_other	8.246
r_dihedral_angle_1_deg	7.626
r_scangle_it	6.744
r_scangle_other	6.744
r_mcangle_it	6.23
r_mcangle_other	6.23
r_scbond_it	4.941
r_scbond_other	4.941
r_mcbond_it	4.787
r_mcbond_other	4.787
r_angle_refined_deg	1.549
r_angle_other_deg	0.518
r_symmetry_nbd_refined	0.266
r_symmetry_nbd_other	0.202
r_nbd_refined	0.199
r_nbd_other	0.191
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.124
r_ncsr_local_group_1	0.111
r_symmetry_nbtor_other	0.09
r_ncsr_local_group_2	0.077
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5557
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	13

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.