X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.0
Details 0.1 M imidazole, 1 M sodium acetate, 1.2-fold molar excess (relative to dimeric protein) of Pro-Tyr-Val-Pst-Ala-Met-Thr (inhibitor), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 26.76 α = 90
b = 86.62 β = 104.6
c = 39.31 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2007-12-13
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8086 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
1.63 43.3 99.0 0.068 -- -- 4.7 21369 21369 -- -3.0 26.01
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)
1.63 1.73 96.3 0.752 -- 1.9 4.2 --

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 1.6324 28.6 -- -- 21365 21365 1070 99.2 0.1715 0.1715 0.1694 0.2124 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 1.6324 1.7066 -- 129 2454 0.2709 0.3062 -- 96.0
X Ray Diffraction 1.7066 1.7966 -- 134 2541 0.2285 0.2729 -- 100.0
X Ray Diffraction 1.7966 1.9092 -- 135 2551 0.2079 0.262 -- 100.0
X Ray Diffraction 1.9092 2.0565 -- 134 2541 0.1716 0.2168 -- 100.0
X Ray Diffraction 2.0565 2.2634 -- 132 2529 0.1508 0.2157 -- 100.0
X Ray Diffraction 2.2634 2.5907 -- 134 2549 0.1722 0.2051 -- 100.0
X Ray Diffraction 2.5907 3.2633 -- 136 2562 0.1543 0.2442 -- 100.0
X Ray Diffraction 3.2633 28.5867 -- 136 2568 0.1522 0.1596 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 28.9429
Anisotropic B[1][1] -0.254
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.3628
Anisotropic B[2][2] -5.9528
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.2068
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.114
f_angle_d 1.77
f_bond_d 0.019
f_dihedral_angle_d 12.592
f_plane_restr 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1520
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 154

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
PHENIX refinement version: 1.7_641
PDB_EXTRACT data extraction version: 3.10
MAR345dtb data collection
XDS data reduction
MR-Rosetta phasing