X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.59 α = 90
b = 62 β = 90
c = 81.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate double crystal monochromator and K-B pair of biomorph mirrors 2007-08-27
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.97937 APS 23-ID-B

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
1.9 62 99.9 0.086 0.093 -- 7.0 24972 24930 -- -- --
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)
1.9 2.0 100.0 0.48 0.52 3.2 7.0 --

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 1.9 49.4 -- -- 24930 23602 1234 99.67 -- 0.21876 0.21635 0.2676 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 1.9 1.949 -- 101 1706 0.344 0.398 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.818
Anisotropic B[1][1] -0.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.31
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.325
r_scbond_it 3.05
r_mcangle_it 3.119
r_mcbond_other 0.184
r_mcbond_it 2.152
r_nbd_refined 0.204
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.071
r_dihedral_angle_4_deg 12.575
r_dihedral_angle_3_deg 14.597
r_dihedral_angle_2_deg 33.015
r_dihedral_angle_1_deg 4.863
r_angle_refined_deg 1.374
r_bond_refined_d 0.009
r_nbd_other 0.186
r_nbtor_refined 0.175
r_nbtor_other 0.083
r_xyhbond_nbd_refined 0.181
r_xyhbond_nbd_other 0.004
r_metal_ion_refined 0.254
r_symmetry_vdw_refined 0.114
r_symmetry_vdw_other 0.249
r_symmetry_hbond_refined 0.386
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2159
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 72

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
AMoRE model building
BLU-ICE data collection