Experiment: 3M4Y

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	35% (v/v) MPD, 0.1M acetate (pH 4.5), vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.564	α = 90
b = 127.564	β = 90
c = 105.403	γ = 90

Symmetry
Space Group	P 43 21 2

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	mirrors	2009-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00	NSRRC	BL13B1

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	2.38	30	99.8	0.04	17.7	7.9	35507	35394			50.3

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)
	2.38	2.47	99.9		0.342	5.76	7.9	3482

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VDZ	2.38	24.93	35347	35342	1769	99.84	0.202	0.199	0.259	RANDOM	56.594

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.397
r_dihedral_angle_4_deg	21.331
r_dihedral_angle_3_deg	18.157
r_dihedral_angle_1_deg	7.626
r_scangle_it	3.129
r_scbond_it	1.81
r_angle_refined_deg	1.44
r_mcangle_it	1.339
r_mcbond_it	0.717
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.397
r_dihedral_angle_4_deg	21.331
r_dihedral_angle_3_deg	18.157
r_dihedral_angle_1_deg	7.626
r_scangle_it	3.129
r_scbond_it	1.81
r_angle_refined_deg	1.44
r_mcangle_it	1.339
r_mcbond_it	0.717
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4394
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	48

Software

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

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.