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_scangle_it 3.074
r_scbond_it 1.867
r_mcangle_it 3.019
r_mcbond_it 1.855
r_symmetry_hbond_refined 0.808
r_symmetry_vdw_other 0.208
r_symmetry_vdw_refined 0.083
r_bond_refined_d 0.023
r_bond_other_d 0.001
r_angle_refined_deg 2.279
r_angle_other_deg 0.904
r_dihedral_angle_1_deg 4.725
r_chiral_restr 0.126
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_nbd_refined 0.209
r_nbd_other 0.272
r_nbtor_other 0.105
r_xyhbond_nbd_refined 0.19
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection