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_sphericity_bonded 2.546
r_sphericity_free 5.517
r_rigid_bond_restr 1.945
r_scangle_it 3.27
r_scbond_it 3.038
r_mcangle_it 1.794
r_mcbond_other 0.548
r_mcbond_it 1.284
r_nbd_refined 0.206
r_gen_planes_other 0.001
r_gen_planes_refined 0.019
r_chiral_restr 0.104
r_dihedral_angle_4_deg 18.526
r_dihedral_angle_3_deg 13.236
r_dihedral_angle_2_deg 39.973
r_dihedral_angle_1_deg 6.727
r_angle_other_deg 2.908
r_angle_refined_deg 1.66
r_bond_other_d 0.002
r_bond_refined_d 0.012
r_nbd_other 0.191
r_nbtor_refined 0.182
r_nbtor_other 0.094
r_xyhbond_nbd_refined 0.182
r_metal_ion_refined 0.097
r_symmetry_vdw_refined 0.244
r_symmetry_vdw_other 0.281
r_symmetry_hbond_refined 0.243
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

Computing
Computing Package Purpose
MARXDS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement