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 Detector
Detector Diffraction Type Details Collection Date
-- -- -- --
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_scangle_it 5.941
r_scbond_it 4.338
r_mcangle_it 12.191
r_mcbond_it 8.367
r_nbd_refined 0.231
r_gen_planes_other 0.003
r_gen_planes_refined 0.015
r_chiral_restr 0.358
r_dihedral_angle_1_deg 7.037
r_angle_other_deg 2.414
r_angle_refined_deg 3.29
r_bond_other_d 0.042
r_bond_refined_d 0.074
r_nbd_other 0.231
r_nbtor_other 0.122
r_xyhbond_nbd_refined 0.118
r_symmetry_vdw_refined 0.886
r_symmetry_vdw_other 0.628
r_symmetry_hbond_refined 0.288
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
AMORE model building