X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details pH 9.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.1 α = 90
b = 133.1 β = 90
c = 133.1 γ = 90
Symmetry
Space Group P 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, Hamburg BW7B

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
3.08 29 99.5 0.0094 -- -- 11.3 -- 625 -- -- --
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)
3.08 3.16 99.9 0.034 -- 2.3 -- --

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 3.1 29.75 -- -- -- 7191 550 99.5 -- 0.284 0.28 0.339 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 3.1 3.18 -- 30 515 0.286 0.306 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.37
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.231
r_symmetry_vdw_other 0.628
r_mcbond_it 8.367
r_symmetry_hbond_refined 0.288
r_bond_other_d 0.042
r_angle_refined_deg 3.29
r_symmetry_vdw_refined 0.886
r_angle_other_deg 2.414
r_bond_refined_d 0.074
r_dihedral_angle_1_deg 7.037
r_nbd_refined 0.231
r_nbtor_other 0.122
r_gen_planes_refined 0.015
r_scbond_it 4.338
r_xyhbond_nbd_refined 0.118
r_chiral_restr 0.358
r_mcangle_it 12.191
r_scangle_it 5.941
r_gen_planes_other 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2133
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 10

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing