X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 34% MPEG 2000, 0.1M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.46 α = 90
b = 54.18 β = 93.88
c = 56.38 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-12-05
Diffraction Radiation
Monochromator Protocol
Mirrors SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9197 ESRF ID14-4

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
1.39 55 95.7 0.054 -- -- 2.9 38354 38354 1.0 1.0 --
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)
1.39 1.44 87.0 0.247 -- 2.6 -- --

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 1.39 55.0 -- 1.0 36789 36789 1544 95.64 0.1809 0.1809 0.18002 0.20178 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 1.39 1.431 -- 73 2331 0.221 0.249 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.18
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.34
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.21
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.436
r_scangle_it 3.843
r_chiral_restr 0.089
r_symmetry_hbond_other 0.04
r_bond_refined_d 0.011
r_dihedral_angle_1_deg 3.299
r_nbd_other 0.215
r_scbond_it 2.566
r_gen_planes_refined 0.025
r_symmetry_vdw_other 0.187
r_angle_other_deg 1.171
r_xyhbond_nbd_other 0.321
r_symmetry_vdw_refined 0.092
r_mcbond_it 0.771
r_nbd_refined 0.267
r_xyhbond_nbd_refined 0.213
r_gen_planes_other 0.073
r_symmetry_hbond_refined 0.215
r_angle_refined_deg 1.373
r_dihedral_angle_3_deg 13.063
r_bond_other_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1668
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 405

Software

Software
Software Name Purpose
DENZO data reduction
SCALA data scaling
SOLVE phasing
REFMAC refinement version: 5.0
CCP4 data scaling version: (SCALA)