X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details 1 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 10 mM nor-NOHA, 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 1 uL precipitant solution (0.1 M MES, pH 6.0, 20% w/v PEG2000 MME) equilibrated against 100 uL precipitant solution using a Nanodrop NS-2 Stage crystallization robot on a 96-well sitting-drop plate (Innovadyne), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.61 α = 90
b = 89.61 β = 90
c = 114.56 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-04-18
Diffraction Radiation
Monochromator Protocol
Cryogenically cooled double-crystal Si(111) with horizontally focusing, sagitally bent second crystal with 4:1 magnification ratio and vertically focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
1.95 50 99.4 0.053 0.053 -- 4.7 24998 24840 0.0 -3.0 --
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)
1.95 2.02 98.1 0.526 0.526 2.917 4.6 --

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 1.95 50.0 -- -- 24998 24016 1795 96.1 0.1418 0.1418 0.1418 0.2008 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 1.95 2.02 2055 165 -- -- -- -- 83.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 41.0
Anisotropic B[1][1] -4.785
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.785
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.57
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.78
c_dihedral_angle_d 22.1
c_angle_deg 1.4
c_bond_d 0.007
c_scangle_it 2.877
c_mcangle_it 2.118
c_scbond_it 1.845
c_mcbond_it 1.249
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.31
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2361
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 137

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building
CBASS data collection