X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 100mM Tris HCl; 2.2M Ammonium Sulfate; 2mM L-Cysteine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.19 α = 90
b = 61.19 β = 90
c = 167 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC -- 2003-11-11
Diffraction Radiation
Monochromator Protocol
Si MAD
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.9807, 0.9808, 0.9537 APS 19-BM
SYNCHROTRON APS BEAMLINE 19-BM 0.9641 APS 19-BM

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
1.4 52.7 0.986 -- 0.051 -- 5.2 69296 69296 -- 1.0 --
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)
1.401 1.45 0.959 -- 0.353 1.5 -- --

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
MAD 1.401 52.7 -- 0.0 69087 65610 3477 99.88 0.16273 0.16273 0.16207 0.17529 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 1.401 1.437 -- 238 4839 0.192 0.185 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.087
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.18
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.54
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.722
r_scbond_it 1.825
r_mcangle_it 1.847
r_mcbond_it 1.102
r_symmetry_hbond_refined 0.245
r_symmetry_vdw_other 0.338
r_symmetry_vdw_refined 0.384
r_bond_refined_d 0.012
r_bond_other_d 0.002
r_angle_refined_deg 1.747
r_angle_other_deg 1.241
r_dihedral_angle_1_deg 8.246
r_chiral_restr 0.122
r_gen_planes_refined 0.007
r_gen_planes_other 0.004
r_nbd_refined 0.29
r_nbd_other 0.24
r_nbtor_other 0.113
r_xyhbond_nbd_refined 0.207
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2161
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 171

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SOLVE model building
SCALEPACK data reduction
HKL-2000 data collection