X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.20M magnesium chloride, 10.00% polyethylene glycol 3000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.64 α = 90
b = 117.64 β = 90
c = 150.12 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2012-08-09
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 -- SSRL BL14-1

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
2.4 29.41 99.9 -- 0.102 -- 7.4 47503 47503 -- -- 52.511
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)
2.4 2.46 100.0 0.722 0.722 2.6 7.5 3468

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
SAD 2.4 29.41 -- 0.0 -- 47455 2400 99.99 -- 0.1972 0.1964 0.2135 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 2.4 2.46 -- 181 3280 0.2105 0.2336 -- 99.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.5116
Anisotropic B[1][1] 5.2001
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.2001
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.4003
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 2.89
t_omega_torsion 3.36
t_angle_deg 1.04
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.368
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4457
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 284

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXD,SHARP 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
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation