Experiment: 3QBY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EAE	pdb entry 3EAE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	291	2.5 M ammonium sulfate, 0.1 M sodium acetate, peptide ligand was added at 0.005 M concentration, pH 4.6, vapor diffusion, temperature 291K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.527	α = 90
b = 41.681	β = 90
c = 156.749	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	CCD	ADSC QUANTUM 210		2009-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.97800	CHESS	A1

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	1.94	25	99.9	0.039	23.4	6.4		21026

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	1.94	1.97	98.3		0.182		5.4	1039

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	pdb entry 3EAE	1.95	20	20561	1055	99.651	0.218	0.2164	0.2528	THIN SHELLS (sftools)	33.681

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]
1.07			0.167		-1.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.319
r_dihedral_angle_4_deg	20.489
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_1_deg	7.048
r_scangle_it	2.547
r_scbond_it	1.658
r_angle_refined_deg	1.21
r_mcangle_it	1.048
r_mcbond_it	0.611
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.319
r_dihedral_angle_4_deg	20.489
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_1_deg	7.048
r_scangle_it	2.547
r_scbond_it	1.658
r_angle_refined_deg	1.21
r_mcangle_it	1.048
r_mcbond_it	0.611
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2034
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.