9RHN | pdb_00009rhn

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WEN

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		292	1.8 M K2HPO4/NaH2PO4, pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.25

Symmetry
Space Group	P 31

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		2024-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.977	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	36.18	99.85	0.1926	0.1978	0.04462	0.998	17.02	19.6		23526

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02			1.086	1.115	0.869	3.26

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	36.18	22519	1111	99.85	0.17754	0.17595	0.1849	0.20885	0.2146	RANDOM	25.078

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]
0.42	0.21		0.42		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.858
r_long_range_B_other	9.414
r_long_range_B_refined	9.401
r_scangle_other	6.971
r_dihedral_angle_1_deg	5.984
r_mcangle_it	5.168
r_mcangle_other	5.167
r_scbond_other	4.85
r_scbond_it	4.841
r_mcbond_it	3.686

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.858
r_long_range_B_other	9.414
r_long_range_B_refined	9.401
r_scangle_other	6.971
r_dihedral_angle_1_deg	5.984
r_mcangle_it	5.168
r_mcangle_other	5.167
r_scbond_other	4.85
r_scbond_it	4.841
r_mcbond_it	3.686
r_mcbond_other	3.684
r_angle_refined_deg	1.029
r_angle_other_deg	0.385
r_chiral_restr	0.047
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2564
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	60

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.