X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details MMP12 at 4mg/ml co-crystallization with AHA and non-chelating inhibitor with precipitant: 19% PEG 10K, 0.2M imidazole malate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.09 α = 90
b = 62.82 β = 90
c = 37.55 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 ADSC QUANTUM 315r mirrors 2009-02-05
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.855 SOLEIL PROXIMA 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
1.31 32.99 100.0 0.101 0.107 -- 9.2 39828 39828 1.0 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)
1.31 1.38 100.0 0.766 0.811 2.9 9.3 --

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
rigid body 1.313 28.594 -- 1.44 39775 39775 1998 99.96 -- 0.1738 0.1726 0.1948 --
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 1.313 1.3458 -- 148 2643 0.2979 0.2806 -- 100.0
X Ray Diffraction 1.3458 1.3822 -- 140 2669 0.262 0.2972 -- 100.0
X Ray Diffraction 1.3822 1.4229 -- 131 2647 0.2369 0.2442 -- 100.0
X Ray Diffraction 1.4229 1.4688 -- 130 2672 0.2254 0.2216 -- 100.0
X Ray Diffraction 1.4688 1.5213 -- 144 2670 0.1936 0.2178 -- 100.0
X Ray Diffraction 1.5213 1.5822 -- 117 2689 0.1877 0.2283 -- 100.0
X Ray Diffraction 1.5822 1.6542 -- 146 2676 0.1812 0.2106 -- 100.0
X Ray Diffraction 1.6542 1.7414 -- 139 2692 0.1681 0.2352 -- 100.0
X Ray Diffraction 1.7414 1.8505 -- 140 2683 0.1649 0.1934 -- 100.0
X Ray Diffraction 1.8505 1.9934 -- 164 2676 0.155 0.1957 -- 100.0
X Ray Diffraction 1.9934 2.1939 -- 144 2700 0.147 0.1778 -- 100.0
X Ray Diffraction 2.1939 2.5112 -- 132 2757 0.1577 0.1802 -- 100.0
X Ray Diffraction 2.5112 3.1632 -- 142 2754 0.1556 0.1737 -- 100.0
X Ray Diffraction 3.1632 28.6005 -- 181 2849 0.151 0.1635 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Anisotropic B[1][1] -0.1565
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.0519
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2084
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.019
f_chiral_restr 0.072
f_dihedral_angle_d 18.144
f_angle_d 1.09
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1246
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 327

Software

Computing
Computing Package Purpose
DNA Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
REFMAC (rigid body) Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine) refinement
REFMAC version: (rigid body) model building
DNA data collection