X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.25
Temperature 300.0
Details Protein solution: 1.4 mM Dlg1 PDZ2, 1.7 mM APC, 100 mM NaCl, 25 mM Tris pH 7.0, 0.1% B-ME Well: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.25, 28% PEG 8000 Drop = 1:1 protein:well solution , VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 27.11 α = 90
b = 51.18 β = 90
c = 71.76 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 210 -- 2007-03-08
Diffraction Radiation
Monochromator Protocol
collected at 1.127 A SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.127 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 70 97.8 -- 0.07 -- 4.0 7000 6846 2.0 2.0 --
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)
2.0 2.07 82.9 -- 0.22 4.8 3.0 590

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 2.0 29.379 -- 0.1 7000 6846 688 95.07 0.1723 0.1723 0.1711 0.1833 10%
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 1.9977 2.1519 -- 116 1067 0.164 0.1872 -- 85.0
X Ray Diffraction 2.1519 2.3683 -- 139 1208 0.1651 0.2035 -- 96.0
X Ray Diffraction 2.3683 2.7108 -- 139 1255 0.1782 0.1913 -- 97.0
X Ray Diffraction 2.7108 3.4146 -- 143 1277 0.1763 0.1821 -- 98.0
X Ray Diffraction 3.4146 29.3823 -- 151 1351 0.1676 0.1678 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.8885
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.5586
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.063
f_dihedral_angle_d 12.794
f_angle_d 0.98
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 769
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 106

Software

Computing
Computing Package Purpose
Blue Ice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
PHENIX model building
Blue version: Ice data collection