X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details Protein:(hMMP12 F171D at 927 micro-M + acetohydroxamic acid at 11.6 milli-M Reservoir: 45% PEG 4,000 0.2 M imidazole piperidine Cryoprotection: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10,000, 10% (AAB buffer 10% acid/90% basic) 0.2 M NaCl. Flash cooling in LN2. , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.92 α = 90
b = 62.89 β = 90
c = 37.7 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 bent cylindrical mirror 2011-01-31
Diffraction Radiation
Monochromator Protocol
horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.8726 ESRF ID23-1

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
1.5 50 99.7 0.114 0.107 -- 7.98 27511 27420 0.0 -3.0 21.127
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)
1.5 1.59 -- 1.094 0.982 2.5 7.92 4379

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 1.5 46.758 -3.0 2.0 27420 27413 1371 99.63 -- 0.1662 0.165 0.1884 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 1.4969 1.5504 2477 130 2477 0.2284 0.2341 -- 97.0
X Ray Diffraction 1.5504 1.6125 2575 136 2575 0.204 0.2207 -- 100.0
X Ray Diffraction 1.6125 1.6859 2571 135 2571 0.1866 0.2466 -- 100.0
X Ray Diffraction 1.6859 1.7747 2593 136 2593 0.1708 0.2135 -- 100.0
X Ray Diffraction 1.7747 1.8859 2590 137 2590 0.1651 0.1725 -- 100.0
X Ray Diffraction 1.8859 2.0316 2575 135 2575 0.1515 0.1909 -- 100.0
X Ray Diffraction 2.0316 2.236 2609 138 2609 0.1564 0.1673 -- 100.0
X Ray Diffraction 2.236 2.5595 2616 137 2616 0.1669 0.203 -- 100.0
X Ray Diffraction 2.5595 3.2246 2651 140 2651 0.1612 0.1837 -- 100.0
X Ray Diffraction 3.2246 46.7812 2785 147 2785 0.1542 0.1706 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 12.02
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.076
f_dihedral_angle_d 16.441
f_angle_d 1.079
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 72
Solvent Atoms 201

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
MOLREP model building
DNA data collection