X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 30% PEG 4K, 0.2M magnesium acetate, 0.1M sodium cacodilate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.09 α = 90
b = 94.09 β = 90
c = 99.29 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2004-04-23
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.93 ESRF ID29

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
2.81 30 90.0 0.1 0.09 -- -- 11820 11173 1.0 1.0 --

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 2.81 30.0 -- -- -- 11173 581 91.67 -- 0.24546 0.24289 0.296 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 2.807 2.879 -- 37 780 0.209 0.354 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.125
Anisotropic B[1][1] 1.03
Anisotropic B[1][2] 0.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.54
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.39
r_scbond_it 2.11
r_mcangle_it 1.523
r_mcbond_it 0.794
r_symmetry_hbond_refined 0.218
r_symmetry_vdw_other 0.282
r_symmetry_vdw_refined 0.231
r_bond_refined_d 0.021
r_bond_other_d 0.002
r_angle_refined_deg 2.116
r_angle_other_deg 0.985
r_dihedral_angle_1_deg 7.977
r_chiral_restr 0.101
r_gen_planes_refined 0.007
r_gen_planes_other 0.003
r_nbd_refined 0.279
r_nbd_other 0.255
r_nbtor_other 0.099
r_xyhbond_nbd_refined 0.196
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3682
Nucleic Acid Atoms 314
Heterogen Atoms 30
Solvent Atoms 7

Software

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