Experiment: 9RVW

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q8Y

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2 M calcium chloride dihydrate, 0.1 M HEPES sodium pH 7.5 and 28% v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.51

Symmetry
Space Group	H 3 2

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 4M		2024-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.2	34.44	98.1	0.994	13.5	10.4		44110

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22			0.794

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	1.2	34.44	44110	2156	98.029	0.173	0.1724	0.1799	0.1853	0.194	12.978

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]
0.305	0.153		0.305		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.182
r_dihedral_angle_3_deg	10.629
r_dihedral_angle_2_deg	8.252
r_dihedral_angle_1_deg	6.731
r_lrange_it	5.37
r_lrange_other	5.123
r_scangle_it	4.131
r_scangle_other	4.129
r_scbond_it	2.707
r_scbond_other	2.705

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.182
r_dihedral_angle_3_deg	10.629
r_dihedral_angle_2_deg	8.252
r_dihedral_angle_1_deg	6.731
r_lrange_it	5.37
r_lrange_other	5.123
r_scangle_it	4.131
r_scangle_other	4.129
r_scbond_it	2.707
r_scbond_other	2.705
r_mcangle_other	2.48
r_mcangle_it	2.465
r_angle_refined_deg	2.023
r_mcbond_it	1.614
r_mcbond_other	1.593
r_angle_other_deg	0.667
r_xyhbond_nbd_refined	0.257
r_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.184
r_nbd_other	0.155
r_symmetry_nbd_refined	0.113
r_chiral_restr	0.112
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1088
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms

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.

9RVW | pdb_00009rvw