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 = 38.51 α = 90
b = 110.94 β = 101.41
c = 67.93 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 -- 2000-09-22
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2

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
1.73 20 96.0 0.057 0.057 -- 2.4 58422 56085 -3.0 -3.0 31.3
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)
1.73 1.78 93.0 0.366 0.366 15.9 2.4 4548

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 1.73 19.69 -- -3.0 58422 50245 5627 96.03 -- 0.17177 0.16654 0.21965 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 1.73 1.775 4548 402 3587 0.209 0.293 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 23.478
Anisotropic B[1][1] -0.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1
Anisotropic B[2][2] 1.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.63
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.16
r_nbd_refined 0.217
r_gen_planes_other 0.013
r_gen_planes_refined 0.016
r_chiral_restr 0.18
r_dihedral_angle_3_deg 18.405
r_dihedral_angle_1_deg 5.766
r_angle_other_deg 1.668
r_angle_refined_deg 2.794
r_bond_other_d 0.001
r_bond_refined_d 0.018
r_xyhbond_nbd_refined 0.192
r_xyhbond_nbd_other 0.093
r_symmetry_vdw_refined 0.239
r_symmetry_vdw_other 0.213
r_symmetry_hbond_refined 0.244
r_mcbond_it 2.598
r_mcangle_it 3.804
r_scbond_it 3.146
r_scangle_it 4.789
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4708
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 576

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
X-PLOR model building
SCALEPACK data reduction
DENZO data collection