X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 294.0
Details PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.29 α = 90
b = 110.99 β = 101.02
c = 67.68 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-04-12
Diffraction Radiation
Monochromator Protocol
double crystal monochromator Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 1.07 SSRL BL1-5

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
1.72 26 78.0 0.056 0.056 -- 4.6 52624 41047 -3.0 -3.0 30.3
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)
1.72 1.82 31.0 0.304 0.304 2.3 2.7 1721

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 1.72 25.73 -- -3.0 52624 41047 4623 77.7 0.17811 0.178 0.17286 0.22571 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 1.72 1.764 1721 102 1019 0.291 0.395 -- 31.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 20.181
Anisotropic B[1][1] -0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.35
Anisotropic B[2][2] 1.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.75
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.76
r_angle_refined_deg 3.034
r_bond_refined_d 0.018
r_nbd_other 0.214
r_dihedral_angle_3_deg 19.417
r_mcbond_it 2.875
r_scbond_it 3.195
r_symmetry_vdw_refined 0.3
r_chiral_restr 0.181
r_xyhbond_nbd_other 0.068
r_symmetry_hbond_refined 0.229
r_angle_other_deg 1.218
r_bond_other_d 0.0
r_dihedral_angle_1_deg 6.081
r_xyhbond_nbd_refined 0.186
r_symmetry_vdw_other 0.26
r_nbd_refined 0.241
r_gen_planes_refined 0.017
r_mcangle_it 3.998
r_gen_planes_other 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4677
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 380

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
X-PLOR model building
REFMAC refinement version: 5.0
X-PLOR phasing