X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.2
Temperature 293.0
Details 3M SODIUM FORMATE, 0.1M SODIUM CITRATE, 5% GLYCEROL, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.95 α = 90
b = 84.57 β = 90
c = 89.32 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 315r -- 2009-03-20
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.979 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
2 50 100.0 0.121 -- -- 4.8 41135 41135 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)
2.0 2.03 100.0 0.758 -- 2.2 4.7 --

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 2.0 44.68 -- -- 39012 39012 2038 99.7 0.17129 0.17129 0.16938 0.20744 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 2.0 2.051 -- 143 2773 0.211 0.243 -- 96.84
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 17.138
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.474
r_scbond_it 1.577
r_mcangle_it 0.875
r_mcbond_it 0.471
r_symmetry_hbond_refined 0.142
r_symmetry_vdw_other 0.299
r_symmetry_vdw_refined 0.211
r_metal_ion_refined 0.097
r_xyhbond_nbd_refined 0.136
r_nbtor_other 0.069
r_nbtor_refined 0.297
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_refined_deg 1.226
r_angle_other_deg 1.241
r_dihedral_angle_1_deg 4.773
r_dihedral_angle_2_deg 32.192
r_dihedral_angle_3_deg 13.732
r_dihedral_angle_4_deg 18.88
r_chiral_restr 0.078
r_gen_planes_refined 0.005
r_nbd_refined 0.191
r_nbd_other 0.204
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3820
Nucleic Acid Atoms 336
Heterogen Atoms 91
Solvent Atoms 335

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.3.0037 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.3.0037 refinement
PHASER model building
HKL-3000 data collection