Experiment: 3RBG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z9M	PDB entry 1Z9M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	0.49 M Sodium Phosphate, 0.91M Potasium Phosphate pH 6.9, Vapor diffusion, Sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.02	α = 90
b = 116.291	β = 90
c = 79.018	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315		2010-09-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	40	98.9	0.076	0.057	12.2	5.5	23676	23676			38.2

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)
1	2.3	2.36	99.8		0.462		5.6	1168

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 1Z9M	2.3	28.47	23571	23571	1190	97.82	0.2001	0.2001	0.1983	0.23	0.2335	0.26	RANDOM	30.1721

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]
-13.73			-10		23.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.054
r_dihedral_angle_4_deg	23.554
r_dihedral_angle_3_deg	15.978
r_dihedral_angle_1_deg	6.622
r_scangle_it	3.313
r_scbond_it	1.96
r_angle_refined_deg	1.442
r_mcangle_it	1.413
r_mcbond_it	0.732
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.054
r_dihedral_angle_4_deg	23.554
r_dihedral_angle_3_deg	15.978
r_dihedral_angle_1_deg	6.622
r_scangle_it	3.313
r_scbond_it	1.96
r_angle_refined_deg	1.442
r_mcangle_it	1.413
r_mcbond_it	0.732
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3146
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	20

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
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.