X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 323.0
Details 8%v/v methyl propane diol, 0.1M Na Acetate, 1mM DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 323K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.47 α = 90
b = 82.47 β = 90
c = 309.89 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 Rosenbaum-Rock monochromator 2001-02-08
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID

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
1.55 40 99.0 0.123 -- -- 5.4 -- 294277 0.0 0.0 --
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)
1.55 1.61 97.0 0.391 -- 2.1 -- 28757

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
FOURIER SYNTHESIS 1.55 40.0 -- 0.0 -- 269565 14342 100.0 0.17535 0.1753 0.17434 0.19441 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 1.55 1.591 -- 1025 19437 0.251 0.266 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.287
Anisotropic B[1][1] 0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.24
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.523
r_scbond_it 1.571
r_mcangle_it 0.834
r_mcbond_it 0.45
r_symmetry_hbond_refined 0.229
r_symmetry_vdw_other 0.238
r_symmetry_vdw_refined 0.336
r_xyhbond_nbd_other 0.477
r_bond_refined_d 0.01
r_bond_other_d 0.001
r_angle_refined_deg 1.389
r_angle_other_deg 0.742
r_dihedral_angle_1_deg 3.816
r_dihedral_angle_3_deg 15.173
r_chiral_restr 0.074
r_gen_planes_refined 0.004
r_gen_planes_other 0.002
r_nbd_refined 0.225
r_nbd_other 0.196
r_xyhbond_nbd_refined 0.157
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13141
Nucleic Acid Atoms 0
Heterogen Atoms 362
Solvent Atoms 1376

Software

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