X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 277.0
Details 20% PEG 3000, 0.2M calcium acetate, 0.1M MIB buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 167.9 α = 90
b = 167.9 β = 90
c = 167.9 γ = 90
Symmetry
Space Group I 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-11-14
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1

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
2.1 83.92 99.4 0.078 -- -- 6.0 -- 23665 -- -- 37.4
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)
2.1 2.1 100.0 0.565 -- 2.8 6.1 3412

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 2.1 41.96 -- -- -- 22426 1215 99.17 -- 0.17375 0.17233 0.20055 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 2.1 2.154 -- 93 1489 0.259 0.303 -- 99.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.906
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.009
r_chiral_restr 0.144
r_dihedral_angle_4_deg 19.269
r_dihedral_angle_3_deg 15.503
r_dihedral_angle_2_deg 35.797
r_dihedral_angle_1_deg 5.739
r_angle_refined_deg 1.668
r_bond_refined_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2172
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 136

Software

Computing
Computing Package Purpose
DNA 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
REFMAC version: 5.6.0117 refinement
MOLREP model building
DNA data collection