X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details HANGING DROPS 20MM TRIS-HCL PH7-8.5, 15-30% POLYETHYLENE GLYCOL 4000, pH 7.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.31 α = 90
b = 122.31 β = 90
c = 82.62 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD MIRRORS --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
2.15 15 100.0 0.09 -- -- 8.9 -- 38032 -- -- --
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)
2.15 2.23 99.9 0.35 -- 7.0 8.7 --

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 2.15 105.41 -- -- -- 35580 1867 98.1 -- 0.194 0.192 0.226 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 2.15 2.21 -- 143 2638 0.2 0.251 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.97
Anisotropic B[1][1] 1.33
Anisotropic B[1][2] 0.66
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.99
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_nbtor_other 0.09
r_scangle_it 3.605
r_symmetry_vdw_refined 0.113
r_dihedral_angle_2_deg 33.75
r_bond_refined_d 0.019
r_mcbond_other 0.238
r_nbd_other 0.198
r_scbond_it 2.602
r_chiral_restr 0.102
r_dihedral_angle_1_deg 6.639
r_mcangle_it 1.498
r_mcbond_it 1.221
r_angle_other_deg 0.88
r_gen_planes_refined 0.007
r_nbd_refined 0.211
r_angle_refined_deg 1.792
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 18.553
r_xyhbond_nbd_refined 0.172
r_symmetry_vdw_other 0.314
r_symmetry_hbond_refined 0.243
r_dihedral_angle_3_deg 15.918
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3084
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 330

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.9999
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing