X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
Temperature 277.0
Details 10.0% PEG-3350, 0.4M Ammonium Tartrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.42 α = 90
b = 128.66 β = 90
c = 133.89 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM -- 2005-10-12
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 -- ALS 8.3.1

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
2.6 29.78 99.8 0.104 0.104 -- 5.4 -- 52320 -- -- 59.22
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)
2.6 2.67 100.0 0.771 0.771 1.0 4.9 --

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 2.6 29.78 -- 0.0 -- 52271 2666 99.64 -- 0.169 0.167 0.204 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 2.6 2.668 3825 211 3614 0.291 0.339 -- 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.565
Anisotropic B[1][1] 5.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.18
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.17
r_dihedral_angle_3_deg 13.623
r_metal_ion_refined 0.192
r_angle_other_deg 0.808
r_mcbond_other 0.382
r_dihedral_angle_4_deg 15.409
r_chiral_restr 0.082
r_nbd_refined 0.191
r_nbtor_other 0.086
r_mcangle_it 2.609
r_angle_refined_deg 1.47
r_symmetry_hbond_refined 0.087
r_symmetry_vdw_other 0.192
r_xyhbond_nbd_refined 0.153
r_scbond_it 4.545
r_nbd_other 0.185
r_symmetry_vdw_refined 0.284
r_bond_other_d 0.001
r_gen_planes_refined 0.005
r_mcbond_it 1.608
r_scangle_it 6.309
r_dihedral_angle_2_deg 30.217
r_gen_planes_other 0.001
r_nbtor_refined 0.179
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5206
Nucleic Acid Atoms 0
Heterogen Atoms 112
Solvent Atoms 312

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
REFMAC refinement version: 5.2.0005
SCALA data scaling
PDB_EXTRACT data extraction version: 1.701
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
MOLREP phasing