X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 289.0
Details 30-35% PEG4000, 0.4 M Magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 21.55 α = 90
b = 43.73 β = 90
c = 77.38 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Mirrors 2001-02-11
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9795 ESRF ID14-4

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
2.5 38.6 98.2 0.1 -- -- 7.8 -- 2787 0.0 0.0 33.26
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)
2.5 2.59 90.4 0.171 -- -- -- --

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 38.63 -- 0.0 2766 2766 126 98.26 0.22151 0.22151 0.21972 0.2579 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 2.565 172 7 172 0.213 0.201 -- 86.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 24.605
Anisotropic B[1][1] -1.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.77
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.214
r_nbd_refined 0.21
r_gen_planes_other 0.004
r_gen_planes_refined 0.008
r_chiral_restr 0.094
r_dihedral_angle_2_deg 20.408
r_dihedral_angle_1_deg 2.791
r_angle_other_deg 0.989
r_angle_refined_deg 1.698
r_bond_other_d 0.001
r_bond_refined_d 0.019
r_xyhbond_nbd_refined 0.495
r_xyhbond_nbd_other 0.222
r_symmetry_vdw_refined 0.096
r_symmetry_vdw_other 0.137
r_symmetry_hbond_refined 0.082
r_mcbond_it 0.867
r_mcangle_it 1.686
r_scbond_it 2.805
r_scangle_it 4.759
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 527
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 28

Software

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