X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 294.0
Details 0.2 M Calcium Acetate, 2-4% PEG 4000, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.35 α = 90
b = 124.35 β = 90
c = 44.82 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2005-02-26
Diffraction Radiation
Monochromator Protocol
Si [111], horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.813 EMBL/DESY, Hamburg X11

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
2.03 19.97 99.9 0.076 0.076 -- 12.1 23225 23179 -3.0 -3.0 42.0
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)
2.03 2.06 97.7 0.664 0.664 4.0 8.5 1112

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
SAD 2.03 19.97 0.0 0.0 23225 21964 1188 99.87 0.179 0.179 0.177 0.217 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 2.033 2.085 1629 86 1543 0.252 0.306 -- 98.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.019
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.175
r_scangle_it 6.355
r_bond_other_d 0.008
r_gen_planes_refined 0.006
r_mcbond_it 1.0
r_symmetry_vdw_refined 0.299
r_dihedral_angle_1_deg 10.934
r_scbond_it 4.168
r_nbd_refined 0.243
r_mcbond_other 0.174
r_nbtor_other 0.088
r_mcangle_it 1.557
r_bond_refined_d 0.016
r_dihedral_angle_4_deg 19.926
r_nbd_other 0.199
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.177
r_chiral_restr 0.09
r_symmetry_metal_ion_refined 0.354
r_symmetry_vdw_other 0.265
r_metal_ion_refined 0.171
r_dihedral_angle_2_deg 37.649
r_nbtor_refined 0.175
r_dihedral_angle_3_deg 17.145
r_angle_refined_deg 1.548
r_angle_other_deg 1.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1734
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 163

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 2.000
Auto-Rickshaw phasing