X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 290.0
Details 5mM MES, 1mM CaCl2, 2.5mM benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.55 α = 90
b = 68.55 β = 90
c = 73.33 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirror 2000-08-12
Diffraction Radiation
Monochromator Protocol
Mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.91 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
0.97 20 99.6 -- 0.065 -- -- 225251 116664 0.0 0.0 7.66
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)
0.97 1.0 95.5 -- 0.401 3.1 -- --

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 0.97 20.0 0.0 0.0 116664 114997 1167 99.6 0.13773 0.13773 0.13355 0.15683 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 0.973 0.998 -- 78 8046 0.309 0.349 -- 95.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.672
Anisotropic B[1][1] -0.15
Anisotropic B[1][2] -0.08
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.23
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.548
r_scbond_it 3.038
r_dihedral_angle_4_deg 18.526
r_metal_ion_refined 0.097
r_sphericity_free 5.517
r_angle_other_deg 2.908
r_nbd_refined 0.206
r_rigid_bond_restr 1.945
r_chiral_restr 0.104
r_nbtor_other 0.094
r_bond_refined_d 0.012
r_mcangle_it 1.794
r_symmetry_vdw_refined 0.244
r_nbd_other 0.191
r_bond_other_d 0.002
r_symmetry_vdw_other 0.281
r_dihedral_angle_2_deg 39.973
r_sphericity_bonded 2.546
r_dihedral_angle_3_deg 13.236
r_dihedral_angle_1_deg 6.727
r_angle_refined_deg 1.66
r_xyhbond_nbd_refined 0.182
r_symmetry_hbond_refined 0.243
r_gen_planes_other 0.001
r_gen_planes_refined 0.019
r_mcbond_it 1.284
r_scangle_it 3.27
r_nbtor_refined 0.182
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 105
Solvent Atoms 449

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
MARXDS data reduction
SCALEPACK data scaling
AMoRE phasing