X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details Tris, MgCl2, PEG 1500, pH 6.0, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75 α = 90
b = 75 β = 90
c = 153.61 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2005-11-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 1.115 MAX II I911-3

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
2.26 31.77 99.8 0.065 0.065 -- 5.6 -- 15045 -- -- --
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)
2.26 2.38 100.0 0.294 0.294 2.6 5.6 2174

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 2.26 31.77 -- 0.0 -- 15043 760 99.73 0.194 -- 0.192 0.241 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 2.26 2.319 1109 60 1049 0.252 0.313 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.279
Anisotropic B[1][1] -2.07
Anisotropic B[1][2] -1.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.11
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.775
r_angle_refined_deg 1.583
r_dihedral_angle_1_deg 7.483
r_nbtor_refined 0.309
r_bond_refined_d 0.014
r_symmetry_vdw_refined 0.182
r_scangle_it 2.664
r_dihedral_angle_3_deg 17.038
r_gen_planes_refined 0.006
r_metal_ion_refined 0.003
r_symmetry_hbond_refined 0.153
r_nbd_refined 0.207
r_xyhbond_nbd_refined 0.153
r_dihedral_angle_4_deg 19.614
r_mcbond_it 0.748
r_dihedral_angle_2_deg 35.623
r_chiral_restr 0.101
r_mcangle_it 1.279
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2530
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 72

Software

Software
Software Name Purpose
SCALA data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MOSFLM data reduction
CCP4 data scaling version: (SCALA)