X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.15
Temperature 293.0
Details 1.85 M SODIUM PHOSPHATE, 0.15 M POTASSIUM PHOSPHATE, pH 4.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.55 α = 90
b = 81.55 β = 90
c = 343.49 γ = 120
Symmetry
Space Group P 61 2 2

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
1.95 50 99.6 0.092 -- -- 11.4 50802 50802 0.0 0.0 19.8
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)
1.95 1.98 100.0 -- -- 2.3 10.7 2481

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 1.95 40.79 -- -- 50802 43621 2348 90.78 0.17884 0.17884 0.17619 0.22893 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 1.95 2.001 -- 81 1301 0.181 0.253 -- 38.06
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 14.607
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.868
r_scbond_it 2.412
r_mcangle_it 1.273
r_mcbond_it 0.754
r_symmetry_metal_ion_refined 0.222
r_symmetry_hbond_refined 0.164
r_symmetry_vdw_refined 0.296
r_bond_refined_d 0.016
r_angle_refined_deg 1.443
r_dihedral_angle_1_deg 5.134
r_dihedral_angle_2_deg 32.263
r_dihedral_angle_3_deg 14.509
r_dihedral_angle_4_deg 24.317
r_chiral_restr 0.099
r_gen_planes_refined 0.006
r_nbd_refined 0.217
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.173
r_metal_ion_refined 0.212
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3817
Nucleic Acid Atoms 0
Heterogen Atoms 114
Solvent Atoms 329

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