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_scangle_it 3.029
r_scbond_it 1.921
r_mcangle_it 1.148
r_mcbond_it 0.636
r_symmetry_hbond_refined 0.272
r_symmetry_vdw_other 0.341
r_symmetry_vdw_refined 0.199
r_bond_refined_d 0.013
r_bond_other_d 0.003
r_angle_refined_deg 1.417
r_angle_other_deg 1.153
r_dihedral_angle_1_deg 6.168
r_chiral_restr 0.115
r_gen_planes_refined 0.006
r_gen_planes_other 0.003
r_nbd_refined 0.227
r_nbd_other 0.253
r_nbtor_other 0.087
r_xyhbond_nbd_refined 0.27
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement