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_scangle_it 5.065
r_scbond_it 3.101
r_mcangle_it 2.326
r_mcbond_it 1.299
r_symmetry_hbond_refined 0.248
r_bond_refined_d 0.007
r_angle_refined_deg 1.066
r_dihedral_angle_1_deg 4.647
r_dihedral_angle_2_deg 34.586
r_dihedral_angle_3_deg 19.616
r_dihedral_angle_4_deg 17.366
r_chiral_restr 0.087
r_gen_planes_refined 0.003
r_nbd_refined 0.204
r_nbtor_refined 0.308
r_xyhbond_nbd_refined 0.15
r_symmetry_vdw_refined 0.179
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

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
Molrep model building
DNA data collection