X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 10MG/ML N-SUC-ALA-LEU-PRO-PHE-PNA, 2M AMMONIUM SULFATE, 5 % PEG 400, 100MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.4 α = 90
b = 111.4 β = 90
c = 111.4 γ = 90
Symmetry
Space Group I 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2009-06-12
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.9841 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
2.55 20 99.7 0.05 0.054 -- 7.35 7658 7636 0.0 -3.0 68.806
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)
2.55 2.65 100.0 0.643 0.662 3.5 7.2 808

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
FOURIER SYNTHESIS 2.55 19.693 0.0 1.24 -- 7636 731 99.93 -- 0.207 0.205 0.235 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 2.55 2.609 -- 49 923 0.288 0.278 -- 100.0
X Ray Diffraction 2.609 2.675 -- 48 914 0.289 0.391 -- 99.0
X Ray Diffraction 2.675 2.747 -- 48 923 0.292 0.367 -- 100.0
X Ray Diffraction 2.747 2.827 -- 49 899 0.262 0.344 -- 100.0
X Ray Diffraction 2.827 2.918 -- 49 940 0.225 0.264 -- 100.0
X Ray Diffraction 2.918 3.022 -- 48 913 0.222 0.218 -- 100.0
X Ray Diffraction 3.022 3.143 -- 48 906 0.213 0.315 -- 100.0
X Ray Diffraction 3.143 3.285 -- 51 951 0.183 0.151 -- 100.0
X Ray Diffraction 3.285 3.458 -- 46 892 0.163 0.239 -- 100.0
X Ray Diffraction 3.458 3.673 -- 50 936 0.189 0.312 -- 100.0
X Ray Diffraction 3.673 3.954 -- 50 923 0.182 0.191 -- 100.0
X Ray Diffraction 3.954 4.348 -- 47 900 0.16 0.21 -- 100.0
X Ray Diffraction 4.348 4.969 -- 49 928 0.139 0.186 -- 100.0
X Ray Diffraction 4.969 6.227 -- 48 920 0.17 0.164 -- 100.0
X Ray Diffraction 6.227 19.694 -- 51 925 0.254 0.225 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 94.308
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.271
f_plane_restr 0.004
f_angle_d 0.928
f_bond_d 0.023
f_chiral_restr 0.058
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.36
Luzzati Resolution Cutoff (Low) 8.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1160
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 21

Software

Software
Software Name Purpose
XSCALE data processing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.005
MAR345dtb data collection
XDS data reduction
XSCALE data scaling