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 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.58 α = 90
b = 49.58 β = 90
c = 116.04 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 -- 2010-07-28
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
1.37 50 97.0 0.05 -- -- 10.5 18054 17494 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)
1.37 1.42 79.8 0.429 -- 2.3 4.3 --

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 1.37 42.93 -- -- -- 17008 924 96.7 -- 0.134 0.133 0.148 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 1.37 1.41 -- 56 966 0.257 0.255 -- 76.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.78
Anisotropic B[1][1] 1.1
Anisotropic B[1][2] 0.55
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.65
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 4.134
r_scangle_it 9.236
r_scbond_it 6.916
r_mcangle_it 5.169
r_mcbond_it 3.781
r_gen_planes_refined 0.015
r_chiral_restr 0.118
r_dihedral_angle_4_deg 25.8
r_dihedral_angle_3_deg 15.722
r_dihedral_angle_2_deg 43.9
r_dihedral_angle_1_deg 6.025
r_angle_refined_deg 1.541
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 667
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 49

Software

Computing
Computing Package Purpose
MXDC Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER-MR 2.1.4 Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHASER-MR version: 2.1.4 model building
MXDC data collection