Experiment: 3R05

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
4.04	69.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.03	α = 89.6
b = 114.574	β = 89.98
c = 160.129	γ = 87.96

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		CCD	MARMOSAIC 300 mm CCD		2010-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1272	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	2.95	50	98.4	0.09	10	3.4		89668

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	2.95	3	95.6		0.532		3.1	4356

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 3QCW	2.95	44.29	89495	4654	98.15	0.2097	0.2083	0.2353	RANDOM	92.1204

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]
-7.06	0.84	-1.09	-2.87	-0.42	9.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.83
r_dihedral_angle_3_deg	20.69
r_dihedral_angle_4_deg	20.317
r_dihedral_angle_1_deg	9.096
r_scangle_it	2.787
r_angle_refined_deg	2.335
r_scbond_it	1.902
r_mcangle_it	1.187
r_mcbond_it	0.717
r_nbtor_refined	0.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.83
r_dihedral_angle_3_deg	20.69
r_dihedral_angle_4_deg	20.317
r_dihedral_angle_1_deg	9.096
r_scangle_it	2.787
r_angle_refined_deg	2.335
r_scbond_it	1.902
r_mcangle_it	1.187
r_mcbond_it	0.717
r_nbtor_refined	0.336
r_symmetry_vdw_refined	0.288
r_symmetry_hbond_refined	0.279
r_nbd_refined	0.26
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.139
r_bond_refined_d	0.026
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15466
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	56

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 R01GM133198.