X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details Mg formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.49 α = 90
b = 105.49 β = 90
c = 374.99 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 243
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-03-20
Diffraction Radiation
Monochromator Protocol
synchrotron SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.921 APS 14-BM-C

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
3.3 20 -- -- -- -- -- -- 33066 2.0 2.0 --
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)
3.3 3.383 99.1 -- -- -- -- --

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 3.3 15.0 -- 0.0 33066 30824 1653 100.0 -- 0.24974 0.24776 0.28756 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 3.3 3.382 -- 122 2125 0.296 0.388 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.536
Anisotropic B[1][1] -0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.21
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.056
r_symmetry_vdw_refined 0.45
r_xyhbond_nbd_refined 0.255
r_bond_refined_d 0.045
r_angle_refined_deg 3.1
r_dihedral_angle_1_deg 4.98
r_dihedral_angle_3_deg 22.942
r_chiral_restr 0.174
r_gen_planes_refined 0.011
r_nbd_refined 0.358
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9930
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 0

Software

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