X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details 0.1M sodium citrate pH 5.6, 20% 2-propanol, 20% polyethylene glycol 4000, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.51 α = 90
b = 105.51 β = 90
c = 361.57 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD double crystal monochromator 2012-05-03
Diffraction Radiation
Monochromator Protocol
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97925 SSRL BL9-2

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
2.5 29.97 99.9 -- 0.09 -- 4.0 78283 78283 -- -- 56.569
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)
2.5 2.56 100.0 0.63 0.63 1.2 3.9 5798

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 2.5 29.965 -- 0.0 -- 78165 3933 99.94 -- 0.1775 0.1759 0.2093 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 2.5 2.56 -- 199 5584 0.2054 0.2354 -- 99.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 65.1717
Anisotropic B[1][1] -2.7827
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.7827
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.5654
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_omega_torsion 3.8
t_angle_deg 1.15
t_other_torsion 2.59
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.397
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14029
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 399

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SOLVE phasing
SCALA data scaling version: 3.3.20
BUSTER-TNT refinement version: 2.10.0
MOSFLM data reduction
BUSTER refinement version: 2.10.0