9RV0 | pdb_00009rv0

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JV0

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	296	28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.73

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 PILATUS 6M		2024-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.69	46.61	93.1	0.104	0.109	0.998	13.81	11.8		55762

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	1.69	1.73	81.3		2.468	2.615	0.332	0.87	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	NONE	1.69	46.61	55649	2755	92.908	0.23	0.2279	0.2343	0.2719	0.2773	31.101

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]
0.009			-0.021		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.396
r_dihedral_angle_4_deg	15.092
r_dihedral_angle_3_deg	15.007
r_dihedral_angle_1_deg	7.996
r_lrange_other	7.308
r_lrange_it	7.301
r_scangle_it	4.918
r_scangle_other	4.917
r_mcangle_it	3.46
r_mcangle_other	3.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.396
r_dihedral_angle_4_deg	15.092
r_dihedral_angle_3_deg	15.007
r_dihedral_angle_1_deg	7.996
r_lrange_other	7.308
r_lrange_it	7.301
r_scangle_it	4.918
r_scangle_other	4.917
r_mcangle_it	3.46
r_mcangle_other	3.46
r_scbond_it	3.235
r_scbond_other	3.235
r_mcbond_it	2.485
r_mcbond_other	2.478
r_angle_refined_deg	1.569
r_angle_other_deg	1.297
r_nbd_other	0.206
r_symmetry_xyhbond_nbd_refined	0.2
r_nbd_refined	0.198
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.169
r_metal_ion_refined	0.162
r_symmetry_nbd_refined	0.161
r_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4016
Nucleic Acid Atoms
Solvent Atoms	126
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.