X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 292.0
Details 2.4 M ammonium sulfate, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.58 α = 90
b = 160.27 β = 90
c = 44.93 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-12-02
Diffraction Radiation
Monochromator Protocol
Si - 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1

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
1.8 24.61 94.7 0.057 -- -- -- -- 50109 -- -- --
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)
1.8 1.9 99.2 0.479 -- 2.9 4.8 7505

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
PDB ENTRY 3DPO 1.8 24.61 -- -- -- 48997 1020 94.56 -- 0.19812 0.1973 0.23762 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 1.8 1.847 -- 57 3405 0.273 0.31 -- 98.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.591
Anisotropic B[1][1] -1.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.04
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.019
r_angle_refined_deg 1.89
r_dihedral_angle_4_deg 18.498
r_dihedral_angle_2_deg 42.689
r_chiral_restr 0.135
r_dihedral_angle_3_deg 16.251
r_dihedral_angle_1_deg 5.034
r_gen_planes_refined 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3356
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 335

Software

Software
Software Name Purpose
marccd data collection
REFMAC refinement version: with PDBID 3DPO
XDS data reduction
SCALA data scaling
REFMAC phasing version: with PDBID 3DPO