X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.09 α = 90
b = 56.46 β = 90
c = 105.35 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 ADSC QUANTUM 4 mirrors 2002-04-21
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 1.1000 NSLS X8C

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
1.3 52.7 97.9 0.05 -- -- 4.62 58507 58507 -- -3.0 12.6
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)
1.3 1.38 87.1 0.498 -- 2.86 -- 5121

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 1.3 52.7 0.0 0.0 55502 55502 2945 98.61 0.17806 0.17806 0.17722 0.19339 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 1.303 1.337 -- 177 3833 0.234 0.249 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 13.417
Anisotropic B[1][1] -0.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.698
r_nbd_other 0.225
r_nbd_refined 0.311
r_gen_planes_other 0.003
r_gen_planes_refined 0.005
r_chiral_restr 0.282
r_dihedral_angle_3_deg 19.138
r_dihedral_angle_1_deg 4.643
r_angle_other_deg 0.854
r_angle_refined_deg 1.541
r_bond_other_d 0.001
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.166
r_symmetry_vdw_refined 0.265
r_symmetry_vdw_other 0.231
r_symmetry_hbond_refined 0.174
r_mcbond_it 1.021
r_mcangle_it 1.762
r_scbond_it 2.258
r_scangle_it 3.586
r_rigid_bond_restr 1.179
r_sphericity_free 2.292
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1997
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 247

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement