X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 292.0
Details NH42SO4,Tris/HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.06 α = 90
b = 73.06 β = 90
c = 111.11 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 1999-09-07
Diffraction Radiation
Monochromator Protocol
Yale Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.95 30 95.2 -- 0.04 -- 9.3 -- 11321 0.0 3.0 26.7
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)
1.95 2.02 92.7 -- 0.328 4.2 -- --

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 1.95 24.5 -- 0.0 11321 10244 518 95.13 0.16032 0.16032 0.15804 0.20492 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 1.952 2.003 -- 33 729 0.173 0.189 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 7.708
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.45
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.205
r_scbond_it 1.632
r_mcangle_it 0.904
r_mcbond_it 0.602
r_symmetry_hbond_refined 0.181
r_symmetry_vdw_other 0.32
r_symmetry_vdw_refined 0.143
r_bond_refined_d 0.015
r_bond_other_d 0.003
r_angle_refined_deg 1.486
r_angle_other_deg 0.789
r_dihedral_angle_1_deg 6.752
r_chiral_restr 0.092
r_gen_planes_refined 0.007
r_gen_planes_other 0.005
r_nbd_refined 0.215
r_nbd_other 0.262
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.188
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.132
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 894
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 144

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