Experiment: 4OPJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D0P	PDB ENTRY 3D0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	0.1 M sodium acetate, 10% w/v PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.387	α = 100.87
b = 47.501	β = 101.77
c = 55.216	γ = 89.75

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2007-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.541	53.054	92.5	0.048	19.52			56542		5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.541	1.65	86.6		4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB ENTRY 3D0P	1.541	53.05	5	52150	4392	92.44	0.1668	0.16212	0.17	0.22007	0.22	RANDOM	32.695

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]
-2.06	-0.6	-0.18	3.82	-3.57	-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.915
r_sphericity_free	32.797
r_sphericity_bonded	26.446
r_dihedral_angle_4_deg	15.982
r_dihedral_angle_3_deg	15.73
r_rigid_bond_restr	8.505
r_scbond_it	8.438
r_long_range_B_refined	8.264
r_mcangle_it	6.141
r_dihedral_angle_1_deg	5.947

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.915
r_sphericity_free	32.797
r_sphericity_bonded	26.446
r_dihedral_angle_4_deg	15.982
r_dihedral_angle_3_deg	15.73
r_rigid_bond_restr	8.505
r_scbond_it	8.438
r_long_range_B_refined	8.264
r_mcangle_it	6.141
r_dihedral_angle_1_deg	5.947
r_mcbond_it	5.339
r_angle_refined_deg	2.054
r_chiral_restr	0.145
r_bond_refined_d	0.022
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms	492
Solvent Atoms	170
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MD2	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.