X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details CO-CRYSTALLIZATION WITH COMPOUND NVP-BLZ295 ADDED BEFORE CONCENTRATION OF THE PROTEIN AT 3 FOLD MOLAR EXCESS. 8% PEG 4000, 0.05 M MES PH 6.5, 0.01 M MGCL2. PROTEIN AT 10.0 MG/ML. CRYOPROTECTION: 30% GLYCEROL + WELL SOLUTION, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.72 α = 90
b = 71.99 β = 90
c = 107.8 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD SAGITALLY FOCUSED SI(III) 2006-12-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA

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 59.87 99.9 0.076 -- -- 5.7 17103 17080 -- -3.0 32.67
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 99.8 0.363 -- 3.84 4.0 1256

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
MOLECULAR REPLACEMENT 2.2 59.87 -- 0.0 -- 17080 854 99.87 -- 0.182 0.1802 0.2153 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 2.33 -- 133 2545 0.1847 0.2253 -- 99.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.27
Anisotropic B[1][1] 8.085
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2325
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.8525
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_angle_deg 0.94
t_omega_torsion 3.19
t_other_torsion 2.63
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.225
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2195
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 139

Software

Software
Software Name Purpose
PHASER phasing
BUSTER refinement version: 2.9.6
XDS data reduction
XSCALE data scaling