X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Details 3MG/ML PROTEIN VAPOUR DIFFUSION WITH MOTHER LIQUOR: 5% PEG8000, 0.1 M TRIS-HCL, PH8.5, pH 8.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.06 α = 90
b = 111.06 β = 90
c = 111.06 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-11-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I711 -- MAX II I711

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
1.88 45 100.0 0.042 -- -- 11.2 -- 37385 -- -- --
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)
1.88 1.92 99.9 0.136 -- 21.0 -- --

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
SIRAS 1.88 19.65 -- -- -- 35449 1861 100.0 -- 0.148 0.147 0.184 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 1.88 1.93 -- 134 2573 0.158 0.219 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.66
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.887
r_scbond_it 2.947
r_mcangle_it 1.936
r_mcbond_it 1.02
r_nbd_refined 0.193
r_gen_planes_other 0.003
r_gen_planes_refined 0.007
r_chiral_restr 0.176
r_dihedral_angle_1_deg 6.816
r_angle_other_deg 0.926
r_angle_refined_deg 1.637
r_bond_other_d 0.002
r_bond_refined_d 0.018
r_nbd_other 0.243
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.173
r_symmetry_vdw_refined 0.363
r_symmetry_vdw_other 0.31
r_symmetry_hbond_refined 0.295
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2879
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 398

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SOLVE model building