X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 294.0
Details PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.9 α = 90
b = 109.3 β = 99.7
c = 67.7 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
IMAGE PLATE MARRESEARCH -- 1997-05-15
Diffraction Radiation
Monochromator Protocol
Single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 1.0 SSRL BL9-1

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
1.9 67 94.0 0.054 0.054 -- 5.9 39417 37052 -3.0 -3.0 34.2
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)
1.9 1.93 82.0 0.352 0.352 3.0 3.1 1782

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 1.9 67.42 -- -3.0 39417 37052 3894 94.0 0.17005 0.17 0.16334 0.2324 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 1.9 1.949 1782 186 2270 0.183 0.253 -- 81.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 24.56
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.24
Anisotropic B[2][2] 0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.28
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 19.59
r_symmetry_hbond_refined 0.205
r_xyhbond_nbd_refined 0.19
r_gen_planes_other 0.015
r_angle_refined_deg 2.922
r_scbond_it 3.461
r_gen_planes_refined 0.019
r_scangle_it 5.125
r_symmetry_vdw_refined 0.113
r_dihedral_angle_1_deg 5.758
r_symmetry_vdw_other 0.137
r_nbd_other 0.144
r_nbd_refined 0.206
r_mcangle_it 4.317
r_angle_other_deg 2.134
r_nbtor_other 0.003
r_bond_other_d 0.002
r_chiral_restr 0.196
r_mcbond_it 3.006
r_bond_refined_d 0.018
r_xyhbond_nbd_other 0.032
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4779
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 584

Software

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