X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details Ammonium sulfate, Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.36 α = 90
b = 81.36 β = 90
c = 72.97 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU OSMIC BLUE 2003-09-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

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
1.85 70.53 96.6 0.079 -- -- 6.5 23397 23397 1.0 1.0 --
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)
1.85 1.92 88.9 0.451 -- 2.51 3.8 --

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 1.85 30.0 -- 1.0 21324 21324 1157 92.82 -- 0.2112 0.21031 0.22831 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 1.85 1.898 -- 66 1300 0.266 0.313 -- 77.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.544
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] -0.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.34
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.191
r_symmetry_hbond_refined 0.084
r_scangle_it 3.783
r_angle_refined_deg 1.268
r_chiral_restr 0.095
r_nbtor_refined 0.313
r_scbond_it 2.517
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 19.434
r_mcbond_it 1.321
r_dihedral_angle_1_deg 4.103
r_nbd_refined 0.246
r_xyhbond_nbd_refined 0.132
r_dihedral_angle_3_deg 14.351
r_bond_refined_d 0.013
r_mcangle_it 1.649
r_dihedral_angle_2_deg 35.379
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1665
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 80

Software

Software
Software Name Purpose
REFMAC refinement version: OF CCP4I FOR FINAL REFINEMENT
CNS refinement
CrystalClear data collection
DENZO data reduction
SCALEPACK data scaling
CNS phasing
REFMAC phasing version: OF CCP4I FOR FINAL REFINEMENT