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_other_torsion 2.59
t_omega_torsion 3.8
t_angle_deg 1.15
t_bond_d 0.01
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SOLVE Structure Solution
BUSTER 2.10.0 Structure Refinement
Software
Software Name Purpose
BUSTER-TNT version: 2.10.0 refinement
SCALA version: 3.3.20 phasing
SOLVE phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation