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_dihedral_angle_2_deg 35.797
r_chiral_restr 0.144
r_dihedral_angle_1_deg 5.739
r_dihedral_angle_4_deg 19.269
r_angle_refined_deg 1.668
r_bond_refined_d 0.022
r_dihedral_angle_3_deg 15.503
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

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