X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 0.16M zinc acetate, 20.0% Glycerol, 14.4% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.51 α = 90
b = 120.51 β = 90
c = 120.51 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2013-07-19
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795,0.9116,0.9792 SSRL BL12-2

Data Collection

Overall
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
2.2 38.11 99.7 -- 0.124 -- 5.1 29737 29737 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.2 2.26 99.9 0.011 1.073 1.6 5.2 2150

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MAD 2.2 38.108 -- 0.0 -- 29664 1506 99.34 -- 0.1987 0.1965 0.2404 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2 2.257 -- 122 1996 0.275 0.303 -- 98.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.1296
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.695
r_mcbond_it 1.62
r_angle_refined_deg 0.968
r_dihedral_angle_4_deg 12.063
r_mcbond_other 1.596
r_dihedral_angle_2_deg 37.336
r_chiral_restr 0.054
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_mcangle_it 2.57
r_dihedral_angle_1_deg 4.957
r_dihedral_angle_3_deg 12.977
r_bond_other_d 0.001
r_bond_refined_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3691
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 211

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
SCALA data scaling version: 3.3.20
REFMAC refinement version: 5.7.0032
MOSFLM data reduction
SHELXD phasing