X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.5
Temperature 293.0
Details Mg formate, pH 5.5, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 170.42 α = 90
b = 170.42 β = 90
c = 170.42 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 315 -- 2008-04-18
Diffraction Radiation
Monochromator Protocol
Channel-cut double-crystal silicon [111] crystal (5.2-20 keV) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.013 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
3 40 99.7 0.092 -- -- 11.6 -- 8740 0.0 0.0 --
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)
3.0 3.16 100.0 0.667 -- 3.7 12.0 1253

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 3.0 38.11 0.0 0.0 8740 8303 414 99.45 -- 0.19111 0.1888 0.23877 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 3.0 3.079 -- 30 600 0.265 0.348 0.238 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.602
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.326
r_mcbond_it 1.299
r_gen_planes_refined 0.003
r_bond_refined_d 0.007
r_dihedral_angle_1_deg 4.647
r_angle_refined_deg 1.066
r_nbd_refined 0.204
r_scangle_it 5.065
r_xyhbond_nbd_refined 0.15
r_chiral_restr 0.087
r_symmetry_vdw_refined 0.179
r_scbond_it 3.101
r_dihedral_angle_3_deg 19.616
r_dihedral_angle_4_deg 17.366
r_nbtor_refined 0.308
r_dihedral_angle_2_deg 34.586
r_symmetry_hbond_refined 0.248
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1638
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 3

Software

Software
Software Name Purpose
DNA data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
MOSFLM data reduction
SCALA data scaling