Experiment: 3GOJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P4Y	PDB entry 1P4Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	BaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.243	α = 90
b = 24.241	β = 110.17
c = 37.281	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	multilayer optics		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	2.601	15.615	98.6	0.058		2.8	1772	1757	1	1	21.448

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.601	2.668	98.6		0.193	2.18	2.4	6667

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1P4Y	2.6	15.615	1757	1757	74	98.6	0.241	0.241	0.236	0.24	0.347	0.34	RANDOM	21.444

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]
-2.92		0.45	3.29		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.324
r_angle_refined_deg	1.903
r_scbond_it	1.533
r_metal_ion_refined	0.351
r_nbtor_refined	0.333
r_symmetry_metal_ion_refined	0.321
r_xyhbond_nbd_refined	0.272
r_symmetry_hbond_refined	0.24
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.168

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.324
r_angle_refined_deg	1.903
r_scbond_it	1.533
r_metal_ion_refined	0.351
r_nbtor_refined	0.333
r_symmetry_metal_ion_refined	0.321
r_xyhbond_nbd_refined	0.272
r_symmetry_hbond_refined	0.24
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.168
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	23
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	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.