9H6O | pdb_00009h6o

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y6T

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.2M Sodium citrate tribasic dehydrate 0.1MBis-Tris propane 6.5 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.48

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 X 16M		2020-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.969384	MAX IV	BioMAX

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	1.8	86.99	100	0.101	0.106	0.029	0.999	12.7	13.1		67615

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	1.8	1.84	100		2.384	2.482	0.679	0.778	1.1	13.3

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	1.8	64.27	67528	3468	99.935	0.222	0.2193	0.2227	0.268	0.2708	39.115

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]
2.015			2.22		-4.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.137
r_dihedral_angle_3_deg	13.381
r_dihedral_angle_2_deg	12.703
r_dihedral_angle_1_deg	7.959
r_lrange_it	7.176
r_lrange_other	7.175
r_scangle_it	5.873
r_scangle_other	5.858
r_mcangle_it	4.771
r_mcangle_other	4.771

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.137
r_dihedral_angle_3_deg	13.381
r_dihedral_angle_2_deg	12.703
r_dihedral_angle_1_deg	7.959
r_lrange_it	7.176
r_lrange_other	7.175
r_scangle_it	5.873
r_scangle_other	5.858
r_mcangle_it	4.771
r_mcangle_other	4.771
r_scbond_it	4.327
r_scbond_other	4.314
r_mcbond_it	3.697
r_mcbond_other	3.685
r_angle_refined_deg	1.694
r_angle_other_deg	0.584
r_nbd_other	0.217
r_nbd_refined	0.205
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.171
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.139
r_ncsr_local_group_2	0.11
r_symmetry_nbtor_other	0.091
r_ncsr_local_group_1	0.087
r_chiral_restr	0.081
r_symmetry_xyhbond_nbd_other	0.029
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	5423
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	40

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.