X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.7
Temperature 298.0
Details PEG 3000, B-n-octyl-glucopyranoside, glutathione sulfonate, sodium acetate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.62 α = 90
b = 57.17 β = 90
c = 134.93 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1997-09-10
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.54 -- --

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 19.7 87.53 0.042 -- -- -- -- 23318 4.0 -3.0 --

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 19.17 -- 4.0 -- 23318 2563 87.53 0.234 0.20089 0.19452 0.26005 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 1.953 -- 88 807 0.211 0.296 -- 87.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.321
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.24
r_gen_planes_refined 0.008
r_bond_refined_d 0.02
r_gen_planes_other 0.007
r_mcbond_it 1.164
r_symmetry_vdw_other 0.343
r_scbond_it 2.894
r_nbtor_other 0.088
r_angle_refined_deg 1.858
r_scangle_it 4.759
r_nbd_refined 0.223
r_angle_other_deg 1.056
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.171
r_symmetry_vdw_refined 0.16
r_chiral_restr 0.141
r_symmetry_hbond_refined 0.118
r_mcangle_it 2.081
r_nbd_other 0.235
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3107
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 153

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SCALEPACK data reduction
DENZO data collection
AMoRE model building