X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 189.0
Details sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 189K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.43 α = 90
b = 65.43 β = 90
c = 142.73 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2001
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2.3 57 99.0 0.053 -- -- 5.6 -- 16193 5.9 -3.0 45.0
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)
2.3 2.36 99.0 0.306 -- 5.9 5.7 --

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 2.3 15.0 -- 0.0 -- 15310 813 98.93 0.21869 0.21869 0.21571 0.27923 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 2.3 2.358 -- 66 1105 0.253 0.326 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS refinement used
Mean Isotropic B 23.119
Anisotropic B[1][1] 1.92
Anisotropic B[1][2] 0.96
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.88
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.236
r_nbd_refined 0.239
r_gen_planes_other 0.003
r_gen_planes_refined 0.006
r_chiral_restr 0.091
r_dihedral_angle_2_deg 24.167
r_dihedral_angle_1_deg 3.689
r_angle_other_deg 0.802
r_angle_refined_deg 1.718
r_bond_other_d 0.001
r_bond_refined_d 0.019
r_xyhbond_nbd_refined 0.169
r_xyhbond_nbd_other 0.106
r_symmetry_vdw_refined 0.269
r_symmetry_vdw_other 0.264
r_symmetry_hbond_refined 0.563
r_mcbond_it 0.803
r_mcangle_it 1.483
r_scbond_it 2.31
r_scangle_it 3.992
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2327
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 172

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
CNS refinement
REFMAC version: 5.0 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection