X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 298.0
Details 0.1M cacodylate, 0.2M Zn(Ac)2, 18% PEG8000, pH 6.4, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.74 α = 90
b = 84.74 β = 90
c = 317.17 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 315 -- 2007-02-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- 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
2.5 50 92.4 0.075 -- -- 12.6 -- 22508 -- -- --
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 60.2 0.361 -- -- 6.3 1406

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 20.0 -- 0.0 -- 19789 1006 82.32 -- 0.236 0.234 0.277 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 2.575 -- 6 133 0.325 0.319 -- 8.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.342
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_mcbond_it 1.065
r_bond_other_d 0.002
r_dihedral_angle_4_deg 12.387
r_angle_refined_deg 1.152
r_mcangle_it 1.897
r_angle_other_deg 0.833
r_mcbond_other 0.283
r_scbond_it 3.207
r_chiral_restr 0.069
r_gen_planes_refined 0.004
r_bond_refined_d 0.009
r_dihedral_angle_2_deg 32.351
r_dihedral_angle_3_deg 15.688
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 6.405
r_scangle_it 4.639
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3271
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 54

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.4.0066
PDB_EXTRACT data extraction version: 3.005
ADSC data collection version: Quantum