X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 292.0
Details Peg 5000 monomethyl ether, glycerol, tris, jeffamine, potassium chloride, calcium chloride, sodium azide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.65 α = 90
b = 107.84 β = 92.25
c = 83.46 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-03-29
Diffraction Radiation
Monochromator Protocol
Ge 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 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
2.48 99 93.3 0.107 -- -- 3.0 23324 23324 -- -3.0 --
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)
2.48 2.57 46.5 0.359 -- -- 2.2 --

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 2.5 25.0 -- 0.0 23042 16900 1828 81.39 -- 0.291 0.286 0.338 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 2.5 2.635 -- 72 140 0.31 0.39 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained individual isotropic (after TLS refinement)
Mean Isotropic B 28.115
Anisotropic B[1][1] -1.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.09
Anisotropic B[2][2] -0.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.07
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.668
r_bond_refined_d 0.005
r_angle_refined_deg 0.927
r_dihedral_angle_1_deg 3.511
r_chiral_restr 0.046
r_gen_planes_refined 0.002
r_nbd_refined 0.175
r_xyhbond_nbd_refined 0.124
r_symmetry_vdw_refined 0.157
r_symmetry_hbond_refined 0.136
r_mcbond_it 0.431
r_mcangle_it 0.81
r_scbond_it 0.894
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2767
Nucleic Acid Atoms 1556
Heterogen Atoms 0
Solvent Atoms 72

Software

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