X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 294.0
Details MES, EDTA, DTT, NaCl, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.79 α = 90
b = 61.79 β = 90
c = 82.82 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-08-10
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.802 EMBL/DESY, Hamburg X13

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
2.15 40 98.9 0.06 -- -- 5.62 9695 9695 0.0 0.0 33.5
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)
2.15 2.23 99.9 0.323 -- -- -- 952

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 2.15 53.45 0.0 0.0 9229 9229 464 99.23 0.19202 0.19202 0.18942 0.24797 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 2.151 2.207 -- 39 676 0.228 0.363 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.732
Anisotropic B[1][1] 0.4
Anisotropic B[1][2] 0.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.6
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 2.279
r_angle_other_deg 0.904
r_symmetry_vdw_refined 0.083
r_scangle_it 3.074
r_bond_refined_d 0.023
r_dihedral_angle_1_deg 4.725
r_bond_other_d 0.001
r_symmetry_hbond_refined 0.808
r_scbond_it 1.867
r_mcangle_it 3.019
r_xyhbond_nbd_refined 0.19
r_mcbond_it 1.855
r_symmetry_vdw_other 0.208
r_nbd_refined 0.209
r_gen_planes_refined 0.008
r_nbd_other 0.272
r_chiral_restr 0.126
r_gen_planes_other 0.001
r_nbtor_other 0.105
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1476
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 41

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.1.24