X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Under Oil
pH 6.5
Temperature 298.0
Details 2 M sodium formate, 0.1 M MES pH 6.5, batch, under oil, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.93 α = 90
b = 42.93 β = 90
c = 127.49 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CCD ADSC_Q210 -- 2008-03-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM16 0.97752 ESRF BM16

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
1.1 37.19 95.1 0.073 0.073 -- 4.3 29341 27903 0.0 0.0 10.78
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)
1.1 1.14 81.9 0.094 0.094 7.1 2.3 2330

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 1.1 20.0 0.0 0.0 27739 26450 1412 95.35 0.15776 0.158 0.157 0.168 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 1.1 1.128 -- 84 1578 0.308 0.318 -- 79.41
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.748
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] -0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.16
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 10.812
r_scangle_it 11.822
r_dihedral_angle_1_deg 5.454
r_rigid_bond_restr 4.54
r_bond_refined_d 0.022
r_dihedral_angle_4_deg 21.605
r_mcangle_it 6.051
r_angle_refined_deg 1.979
r_chiral_restr 0.151
r_sphericity_free 22.595
r_scbond_it 7.941
r_mcbond_it 3.978
r_dihedral_angle_2_deg 47.403
r_dihedral_angle_3_deg 10.323
r_gen_planes_refined 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 473
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 42

Software

Software
Software Name Purpose
SCALA data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection
HKL-2000 data reduction