X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details 0.16 M Ammonium sulfate, 0.1 M Sodium Acetate, pH 4.6, 18-20% PEG4000, 25% Glycerol, and 10 mM DTT, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.86 α = 90
b = 85.86 β = 90
c = 138.35 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 high-resolution double-crystal monochromator 2008-11-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.00 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 91.5 0.058 -- -- 12.0 45761 42194 1.9 1.9 --
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 2.06 68.0 0.515 -- 1.5 -- --

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 50.0 -- 1.5 41320 37754 802 91.37 0.2126 0.2122 0.2122 0.24807 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 2.06 -- -- 1114 -- -- -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.511
Anisotropic B[1][1] 1.22
Anisotropic B[1][2] 0.61
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.83
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 15.24
r_symmetry_hbond_refined 0.081
r_chiral_restr 0.095
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.131
r_symmetry_vdw_refined 0.322
r_scbond_it 1.747
r_scangle_it 2.728
r_mcangle_it 1.383
r_bond_refined_d 0.011
r_angle_refined_deg 1.308
r_dihedral_angle_1_deg 6.367
r_nbd_refined 0.209
r_nbtor_refined 0.309
r_dihedral_angle_2_deg 37.658
r_dihedral_angle_4_deg 21.719
r_mcbond_it 0.816
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2934
Nucleic Acid Atoms 0
Heterogen Atoms 79
Solvent Atoms 124

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
HKL-2000 data collection
Phaser model building