X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.7
Temperature 293.0
Details 1.6M ammonium sulfate, 100mM cacodylate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.52 α = 90
b = 140.02 β = 122.07
c = 102.71 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 ADSC QUANTUM 4 mirrors 2000-02-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6

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
1.5 38.92 93.11 0.048 -- -- 5.3 210686 196162 4.0 2.0 19.3
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)
1.5 1.53 86.7 0.766 -- 1.56 2.9 9101

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
SIRAS 1.5 38.92 -- 0.0 196162 196162 19515 93.11 0.13594 0.13594 0.1323 0.16869 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 1.5 1.539 10088 1068 10088 0.226 0.287 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic temperature factors
Mean Isotropic B 14.02
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.776
r_scbond_it 4.032
r_gen_planes_refined 0.009
r_gen_planes_other 0.006
r_chiral_restr 0.137
r_angle_other_deg 2.063
r_symmetry_vdw_refined 0.162
r_bond_refined_d 0.018
r_nbtor_other 0.106
r_xyhbond_nbd_refined 0.188
r_bond_other_d 0.002
r_nbd_refined 0.225
r_mcbond_it 1.747
r_mcangle_it 2.547
r_dihedral_angle_1_deg 5.538
r_symmetry_vdw_other 0.338
r_scangle_it 5.741
r_nbd_other 0.25
r_symmetry_hbond_refined 0.154
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.071
Luzzati ESD (R-Free Set) 0.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8236
Nucleic Acid Atoms 0
Heterogen Atoms 270
Solvent Atoms 1333

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.27
DENZO data reduction
SCALEPACK data scaling
CCP4 data scaling version: (TRUNCATE)
MLPHARE phasing
SHELXD phasing
DM phasing
SOLVE phasing