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% PEG3000, 0.15M calcium acetate, 0.1M MIB buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 168.79 α = 90
b = 168.79 β = 90
c = 168.79 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 MARMOSAIC 225 mm CCD mirror 2011-01-01
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2

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
3.15 50 100.0 0.154 -- -- 7.7 -- 7414 -- -- 70.0
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)
3.15 3.32 100.0 0.807 -- 2.5 7.9 1056

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 3.15 50.0 -- -- -- 7036 353 99.91 -- 0.22084 0.2195 0.24838 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 3.15 3.232 -- 24 442 0.302 0.244 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.601
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.004
r_gen_planes_refined 0.002
r_dihedral_angle_2_deg 32.594
r_dihedral_angle_3_deg 13.579
r_angle_refined_deg 0.873
r_dihedral_angle_4_deg 9.918
r_bond_other_d 0.0
r_angle_other_deg 0.217
r_chiral_restr 0.051
r_dihedral_angle_1_deg 4.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2177
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 2

Software

Software
Software Name Purpose
DNA data collection
MOLREP phasing
REFMAC refinement version: 5.6.0117
MOSFLM data reduction
SCALA data scaling