X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 50/50, 200mM NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.11 α = 90
b = 97.94 β = 111.73
c = 46.08 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 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
1.76 50 98.0 0.136 0.119 -- 4.23 32612 31957 0.0 -3.0 24.441
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)
1.76 1.87 94.2 0.666 0.582 2.33 4.13 5246

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 1.764 42.806 -3.0 2.0 31957 31949 1598 98.28 -- 0.1993 0.1964 0.2541 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 1.7642 1.8211 2598 137 2598 0.2696 0.3117 -- 92.0
X Ray Diffraction 1.8211 1.8862 2723 143 2723 0.2343 0.3088 -- 98.0
X Ray Diffraction 1.8862 1.9618 2754 145 2754 0.2077 0.2585 -- 99.0
X Ray Diffraction 1.9618 2.051 2748 145 2748 0.2 0.2444 -- 98.0
X Ray Diffraction 2.051 2.1592 2769 145 2769 0.1875 0.238 -- 99.0
X Ray Diffraction 2.1592 2.2944 2788 147 2788 0.1984 0.2603 -- 99.0
X Ray Diffraction 2.2944 2.4716 2762 146 2762 0.1969 0.3139 -- 99.0
X Ray Diffraction 2.4716 2.7203 2789 146 2789 0.1991 0.2359 -- 99.0
X Ray Diffraction 2.7203 3.1138 2776 146 2776 0.1961 0.2836 -- 99.0
X Ray Diffraction 3.1138 3.9226 2807 148 2807 0.1764 0.2212 -- 100.0
X Ray Diffraction 3.9226 42.8181 2837 150 2837 0.1892 0.2333 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.074
f_dihedral_angle_d 18.451
f_angle_d 1.03
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2608
Nucleic Acid Atoms 0
Heterogen Atoms 121
Solvent Atoms 380

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