X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 5 mg/ml protein added in 50:50 ratio to the well-solution of 25% PEG 4000, 100 mM sodium citrate, 200 mM ammonium sulphate. Crystals grown in the dark due to photosensitivity of the cofactor., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 141.57 α = 90
b = 37.27 β = 105
c = 55.07 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2007-05-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29

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
1.45 32.89 99.3 0.098 -- -- 3.6 -- 49235 0.0 0.0 15.1
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)
1.45 1.53 99.4 0.767 -- 2.2 3.5 7129

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 1.45 32.89 -- -- -- 46662 2455 99.03 -- 0.14859 0.14495 0.21707 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 1.45 1.488 -- 164 3206 0.264 0.364 -- 96.64
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 22.927
Anisotropic B[1][1] 0.34
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.1
Anisotropic B[2][2] -0.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.26
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 19.639
r_sphericity_free 38.308
r_rigid_bond_restr 6.36
r_gen_planes_refined 0.012
r_chiral_restr 0.135
r_dihedral_angle_4_deg 16.794
r_dihedral_angle_3_deg 15.465
r_dihedral_angle_2_deg 36.967
r_dihedral_angle_1_deg 5.763
r_angle_refined_deg 2.052
r_bond_refined_d 0.02
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.04
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2289
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 409

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
MOLREP model building