Experiment: 3PBX

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.89	α = 90
b = 25.001	β = 110.01
c = 37.044	γ = 90

Symmetry
Space Group	C 1 2 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	OXFORD SAPPHIRE CCD	multi-graded optics	2007-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.5418

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	1.879	14.866	78.55	0.045		2.1	4705	3706	1	1	27.446

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.879	1.927

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GOJ	1.879	14.86	3531	175	78.55	0.2544	0.2508	0.32701	RANDOM	27.446

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]
-3.38		0.31	3.36		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.016
r_angle_refined_deg	3.666
r_scbond_it	3.007
r_symmetry_hbond_refined	0.434
r_xyhbond_nbd_refined	0.389
r_nbtor_refined	0.344
r_nbd_refined	0.259
r_metal_ion_refined	0.172
r_chiral_restr	0.15
r_symmetry_vdw_refined	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.016
r_angle_refined_deg	3.666
r_scbond_it	3.007
r_symmetry_hbond_refined	0.434
r_xyhbond_nbd_refined	0.389
r_nbtor_refined	0.344
r_nbd_refined	0.259
r_metal_ion_refined	0.172
r_chiral_restr	0.15
r_symmetry_vdw_refined	0.106
r_bond_refined_d	0.021
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	57
Heterogen Atoms	2

Software

Software
Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	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 R01GM133198.