X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details cadmium sulphate 0.05M, sodium acetate 1.0M, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.63 α = 90
b = 49.63 β = 90
c = 116.31 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 RAYONIX MX300HE -- 2012-06-07
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97921 CLSI 08B1-1

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
1.6 50 99.9 0.058 -- -- 20.4 11929 11912 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)
1.6 1.66 100.0 0.382 -- -- 20.6 1155

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 1.6 42.98 -- 0.0 11234 11795 561 99.35 0.1219 0.122 0.1206 0.1497 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 1.599 1.641 -- 53 782 0.086 0.149 -- 98.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.3211
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 3.425
r_bond_refined_d 0.018
r_angle_refined_deg 1.735
r_dihedral_angle_1_deg 6.612
r_dihedral_angle_2_deg 44.608
r_dihedral_angle_3_deg 15.232
r_dihedral_angle_4_deg 27.846
r_chiral_restr 0.125
r_gen_planes_refined 0.012
r_mcbond_it 3.009
r_mcangle_it 4.468
r_scbond_it 6.293
r_scangle_it 8.967
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 670
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 67

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