X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.7
Temperature 295.0
Details Potassium Phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.81 α = 90
b = 76.3 β = 116.21
c = 98.13 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Mirrors 2000-08-20
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 1.00000 APS 5ID-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
1.71 25 98.1 0.041 -- -- 5.3 83273 83273 -- -3.0 28.4
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)
1.71 1.77 97.0 0.122 -- 10.7 3.6 8238

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 1.71 24.77 0.0 0.0 -- 76559 4052 98.1 -- 0.15552 0.15366 0.19105 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 1.71 1.755 5519 284 5519 0.181 0.211 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.264
Anisotropic B[1][1] 1.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.87
Anisotropic B[2][2] -0.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.09
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.127
r_symmetry_vdw_refined 0.148
r_bond_refined_d 0.017
r_nbd_other 0.223
r_gen_planes_refined 0.013
r_bond_other_d 0.0
r_symmetry_vdw_other 0.22
r_xyhbond_nbd_refined 0.137
r_dihedral_angle_1_deg 8.112
r_mcangle_it 1.911
r_scangle_it 4.785
r_angle_refined_deg 2.09
r_gen_planes_other 0.013
r_angle_other_deg 4.079
r_nbd_refined 0.161
r_scbond_it 3.079
r_symmetry_hbond_refined 0.158
r_nbtor_other 0.113
r_mcbond_it 1.168
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5572
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 806

Software

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