Experiment: 7PCD

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.75	293	18% PEG3350, 50mM ammonium tartrate, 150mM sodium tartrate and 100mM BIS-TRIS

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.009	α = 90
b = 94.471	β = 90
c = 80.325	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

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		2019-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

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	1.77	61.19	95.4	0.064	0.071	0.999	10.65	5.1		24847			37.966

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	1.77	2.02	97.6		0.438	0.038	0.999	3.19	5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3RCD	1.77	61.19	22352	2495	95.41	0.2101	0.2066	0.22	0.2406	0.25	RANDOM	40.971

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]
6.12			-3.19		-2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.267
r_dihedral_angle_4_deg	12.738
r_dihedral_angle_3_deg	12.164
r_dihedral_angle_1_deg	5.906
r_angle_refined_deg	1.438
r_angle_other_deg	1.191
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.267
r_dihedral_angle_4_deg	12.738
r_dihedral_angle_3_deg	12.164
r_dihedral_angle_1_deg	5.906
r_angle_refined_deg	1.438
r_angle_other_deg	1.191
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2176
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	45

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

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.