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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4GQL
Crystal structure of the catalytic domain of Human MMP12 in complex with selective phosphinic inhibitor RXP470.1
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A+S)
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
Reservoir: 25% PEG 10000, 0.2M imidazole malate. Cryoprotectant: 27% PEG 8000, 15% MPEG 550, 10% glycerol, .01M hydroxamic acid, 90mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 69.58
α = 90
b = 63.39
β = 90
c = 36.9
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
2009-02-23
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
0.979300
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
1.15
50
98.6
0.091
0.084
--
6.9
58830
58014
0.0
0.0
13.934
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)
1.15
1.22
96.5
1.3
1.2
2.3
6.73
--
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
1.15
32.599
--
1.99
58014
57994
2900
98.69
--
0.1343
0.1333
0.1545
--
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
1.15
1.1689
--
124
2342
0.312
0.3186
--
91.0
X Ray Diffraction
1.1689
1.189
--
139
2641
0.252
0.232
--
100.0
X Ray Diffraction
1.189
1.2107
--
137
2613
0.2202
0.2341
--
100.0
X Ray Diffraction
1.2107
1.234
--
138
2638
0.2176
0.2582
--
100.0
X Ray Diffraction
1.234
1.2591
--
137
2593
0.1946
0.2375
--
100.0
X Ray Diffraction
1.2591
1.2865
--
139
2649
0.1761
0.2652
--
100.0
X Ray Diffraction
1.2865
1.3164
--
139
2631
0.1642
0.1911
--
100.0
X Ray Diffraction
1.3164
1.3494
--
137
2606
0.1386
0.1624
--
100.0
X Ray Diffraction
1.3494
1.3859
--
139
2638
0.1261
0.1409
--
100.0
X Ray Diffraction
1.3859
1.4266
--
139
2648
0.1182
0.1495
--
100.0
X Ray Diffraction
1.4266
1.4727
--
138
2628
0.1081
0.1307
--
100.0
X Ray Diffraction
1.4727
1.5253
--
139
2634
0.1065
0.1338
--
100.0
X Ray Diffraction
1.5253
1.5864
--
139
2649
0.0982
0.126
--
100.0
X Ray Diffraction
1.5864
1.6586
--
140
2654
0.1016
0.1416
--
100.0
X Ray Diffraction
1.6586
1.746
--
140
2664
0.1061
0.1249
--
100.0
X Ray Diffraction
1.746
1.8554
--
139
2636
0.1091
0.1279
--
100.0
X Ray Diffraction
1.8554
1.9986
--
141
2670
0.1108
0.1214
--
100.0
X Ray Diffraction
1.9986
2.1997
--
141
2695
0.1119
0.1236
--
100.0
X Ray Diffraction
2.1997
2.5179
--
142
2684
0.1189
0.1331
--
100.0
X Ray Diffraction
2.5179
3.1719
--
144
2732
0.1276
0.1492
--
99.0
X Ray Diffraction
3.1719
32.6125
--
129
2449
0.1504
0.1702
--
85.0
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
Anisotropic
RMS Deviations
Key
Refinement Restraint Deviation
f_plane_restr
0.007
f_dihedral_angle_d
15.377
f_bond_d
0.008
f_chiral_restr
0.112
f_angle_d
1.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1246
Nucleic Acid Atoms
0
Heterogen Atoms
57
Solvent Atoms
303
Software
Software
Software Name
Purpose
DNA
data collection
MOLREP
phasing
PHENIX
refinement version: (phenix.refine: 1.8_1069)
XDS
data reduction
XDS
data scaling