X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details cadmium sulphate octahydrate 0.02M, sodium acetate 0.6M, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.25 α = 90
b = 49.25 β = 90
c = 113.38 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-07-21
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
1.9 50 99.7 0.062 -- -- 9.5 7012 6990 2.0 -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)
1.9 1.97 99.8 0.327 -- -- 9.8 662

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 1.9 42.65 -- 0.0 6561 6891 330 98.91 0.1539 0.1433 0.1416 0.1777 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 1.897 1.946 -- 22 454 0.179 0.234 -- 98.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.5142
Anisotropic B[1][1] 0.88
Anisotropic B[1][2] 0.44
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.33
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 3.483
r_bond_refined_d 0.016
r_angle_refined_deg 1.64
r_dihedral_angle_1_deg 6.595
r_dihedral_angle_2_deg 43.376
r_dihedral_angle_3_deg 15.464
r_dihedral_angle_4_deg 22.994
r_chiral_restr 0.109
r_gen_planes_refined 0.01
r_mcbond_it 2.429
r_mcangle_it 3.984
r_scbond_it 6.11
r_scangle_it 9.173
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 674
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 45

Software

Computing
Computing Package Purpose
MxDC Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0109 refinement
HKL data reduction