X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 290.0
Details 26% PEG 4000, 0.2 M Li2SO4, 2% MPD, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.4 α = 90
b = 50.52 β = 90
c = 200.07 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 CUSTOM-MADE -- 2000-06-28
Diffraction Radiation
Monochromator Protocol
Si-111 double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.95007 APS 19-ID

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
1.48 35 99.3 -- 0.049 -- 3.9 -- 82429 -- -3.0 --
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)
1.48 1.5 100.0 -- 0.693 2.0 3.0 2721

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 1.48 34.92 -- 0.0 -- 77790 5912 94.47 -- 0.16404 0.16177 0.19113 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 1.48 1.5 5114 391 -- 0.223 0.248 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 7.66
Anisotropic B[1][1] -0.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.28
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.807
r_nbtor_other 0.357
r_nbd_other 0.207
r_nbd_refined 0.225
r_gen_planes_other 0.002
r_gen_planes_refined 0.007
r_chiral_restr 0.096
r_dihedral_angle_3_deg 16.241
r_dihedral_angle_1_deg 4.698
r_angle_other_deg 1.172
r_angle_refined_deg 1.556
r_bond_other_d 0.001
r_bond_refined_d 0.014
r_xyhbond_nbd_refined 0.174
r_symmetry_vdw_refined 0.098
r_xyhbond_nbd_other 0.25
r_symmetry_vdw_other 0.207
r_symmetry_hbond_refined 0.18
r_symmetry_hbond_other 0.091
r_mcbond_it 0.963
r_mcangle_it 1.413
r_scbond_it 2.072
r_scangle_it 3.049
r_rigid_bond_restr 1.157
r_sphericity_free 5.102
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3152
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 424

Software

Computing
Computing Package Purpose
DENZO 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
AMoRE model building
SCALEPACK data reduction
DENZO data collection