X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 290.0
Details 0.1M citric acid, 1.6M ammonium sulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.79 α = 90
b = 70.79 β = 90
c = 217.12 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic Confocal MaxFlux optic system 2003-03-10
Diffraction Radiation
Monochromator Protocol
osmium 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
1.9 30 98.7 -- 0.082 -- 12.6 26051 25322 2.0 2.0 31.7
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)
1.9 1.92 88.3 -- 0.323 3.011 -- 767

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 30.0 -- 2.0 26051 24733 1325 98.62 -- 0.17379 0.17256 0.19614 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 1.95 -- -- 1641 0.234 0.267 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS refinement
Mean Isotropic B 19.04
Anisotropic B[1][1] 0.54
Anisotropic B[1][2] 0.27
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.81
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.115
r_symmetry_vdw_other 0.341
r_mcangle_it 1.148
r_angle_refined_deg 1.417
r_symmetry_vdw_refined 0.199
r_nbd_refined 0.227
r_scangle_it 3.029
r_mcbond_it 0.636
r_angle_other_deg 1.153
r_xyhbond_nbd_refined 0.27
r_dihedral_angle_1_deg 6.168
r_gen_planes_refined 0.006
r_nbtor_other 0.087
r_gen_planes_other 0.003
r_bond_refined_d 0.013
r_scbond_it 1.921
r_bond_other_d 0.003
r_nbd_other 0.253
r_symmetry_hbond_refined 0.272
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.213
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1777
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 180

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
CNS phasing