X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 294.0
Details 2.1 M ammonium sulphate, 100 mM Tris pH 8.5, 5 mM 5-phosphoarabinonate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.4 α = 90
b = 94.4 β = 90
c = 137.1 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2000-12-15
Diffraction Radiation
Monochromator Protocol
Osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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
2.51 94.4 98.4 0.128 0.128 -- 6.9 21797 21797 0.0 0.0 25.4
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)
2.51 2.59 99.8 0.254 0.254 3.1 6.8 2171

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
REFINEMENT 2.51 50.0 -- 0.0 21468 21468 1101 98.4 0.217 0.217 0.214 0.268 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 2.51 2.565 1572 91 1481 0.223 0.265 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 25.156
Anisotropic B[1][1] -0.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.022
r_scbond_it 1.834
r_bond_refined_d 0.011
r_angle_refined_deg 1.473
r_dihedral_angle_1_deg 3.624
r_dihedral_angle_3_deg 17.246
r_chiral_restr 0.104
r_gen_planes_refined 0.005
r_nbd_refined 0.241
r_xyhbond_nbd_refined 0.174
r_symmetry_vdw_refined 0.202
r_symmetry_hbond_refined 0.348
r_mcbond_it 0.516
r_mcangle_it 1.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4424
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 109

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (intensity integration)
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (data scaling)
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement