X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Counter Diffusion in Capillary
pH 5
Temperature 298.0
Details 3M ammonium sulphate, 0.1M sodium acetate, pH 5, counter-diffusion in capillary, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 187 α = 90
b = 187 β = 90
c = 59.33 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 315r -- 2011-01-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.97 ESRF ID14-4

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
1.85 93.5 98.0 0.071 0.071 -- 3.7 64691 64691 0.0 0.0 18.725
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)
1.85 1.95 96.7 0.483 0.483 1.6 3.4 9332

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 1.85 20.0 0.0 0.0 66037 64691 3283 97.96 0.1802 0.1802 0.178 0.221 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 1.85 1.898 -- 236 4462 0.238 0.29 -- 97.01
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 19.7394
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.07
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.013
r_chiral_restr 0.129
r_dihedral_angle_4_deg 15.016
r_dihedral_angle_3_deg 13.975
r_dihedral_angle_2_deg 37.688
r_dihedral_angle_1_deg 5.809
r_angle_refined_deg 2.411
r_bond_refined_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5088
Nucleic Acid Atoms 0
Heterogen Atoms 435
Solvent Atoms 540

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.3.20 data reduction
Mosflm version: 3.3.20 data collection