X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 34% PEG 2000, 0.1M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.53 α = 90
b = 54.58 β = 116.59
c = 33.23 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-11-09
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
1.8 40 81.3 0.031 -- -- 1.6 7693 7693 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)
1.8 1.9 71.0 0.087 -- 6.9 -- --

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 1.8 38.63 -- 1.0 7693 6730 683 80.74 0.19033 0.19033 0.18379 0.24571 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 1.801 1.847 -- -- 552 0.178 -- -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.038
Anisotropic B[1][1] -0.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.21
Anisotropic B[2][2] 0.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.504
r_scbond_it 2.953
r_mcangle_it 1.429
r_mcbond_it 0.745
r_symmetry_hbond_refined 0.741
r_symmetry_vdw_other 0.264
r_symmetry_vdw_refined 0.19
r_xyhbond_nbd_other 0.138
r_bond_refined_d 0.014
r_bond_other_d 0.001
r_angle_refined_deg 1.479
r_angle_other_deg 0.794
r_dihedral_angle_1_deg 3.962
r_dihedral_angle_3_deg 15.884
r_chiral_restr 0.086
r_gen_planes_refined 0.006
r_gen_planes_other 0.003
r_nbd_refined 0.239
r_nbd_other 0.207
r_xyhbond_nbd_refined 0.266
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 820
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 110

Software

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