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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4H84
Crystal structure of the catalytic domain of Human MMP12 in complex with a selective carboxylate based inhibitor.
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 1 (gz) (A+S)
Biological Assembly 2 (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
Protein: hMMP12 F171D at4 784 mico-M + 10 milli-M AHA Reservoir: 12% PEG 20K, 0.14 M imidazole malate, .0175 M NaCl Cryoprotectant: 40% C7 (C7 = 12.5 % di-ethylene glycol + 12.5 % ethylene glycol + 25 % 1,2-propanediol + 12.5 % DMSO + 12.5 % glycerol), 1M NaCl, 0.1 M (MMT buffer 75% acid/25% basic), 9% PEG 10.000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 42.14
α = 90
b = 62.79
β = 90
c = 113.14
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315r
MIRRORS
2012-06-14
Diffraction Radiation
Monochromator
Protocol
Single Silicon (111)
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID23-1
0.9763
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
1.59
50
98.6
0.159
0.147
--
7.68
41050
40489
0.0
-3.0
21.449
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)
1.59
1.69
92.6
0.957
0.892
3.13
7.47
6540
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
1.592
42.029
-3.0
2.02
40489
40486
2024
98.64
--
0.1729
0.1711
0.2062
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
1.5924
1.6323
2270
120
2270
0.2899
0.3273
--
83.0
X Ray Diffraction
1.6323
1.6764
2774
146
2774
0.2288
0.2873
--
100.0
X Ray Diffraction
1.6764
1.7257
2727
143
2727
0.2056
0.2576
--
100.0
X Ray Diffraction
1.7257
1.7814
2742
144
2742
0.1915
0.2474
--
100.0
X Ray Diffraction
1.7814
1.8451
2770
146
2770
0.1808
0.2029
--
100.0
X Ray Diffraction
1.8451
1.919
2748
145
2748
0.176
0.2114
--
100.0
X Ray Diffraction
1.919
2.0063
2752
145
2752
0.1726
0.1938
--
100.0
X Ray Diffraction
2.0063
2.1121
2774
146
2774
0.1648
0.234
--
100.0
X Ray Diffraction
2.1121
2.2444
2756
145
2756
0.1672
0.2075
--
100.0
X Ray Diffraction
2.2444
2.4177
2779
146
2779
0.1671
0.2229
--
100.0
X Ray Diffraction
2.4177
2.6609
2797
147
2797
0.1627
0.1844
--
100.0
X Ray Diffraction
2.6609
3.0459
2802
148
2802
0.1618
0.2028
--
100.0
X Ray Diffraction
3.0459
3.8371
2859
150
2859
0.1484
0.1817
--
100.0
X Ray Diffraction
3.8371
42.0431
2912
153
2912
0.1612
0.1748
--
98.0
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
Isotropic
Mean Isotropic B
21.4
RMS Deviations
Key
Refinement Restraint Deviation
f_angle_d
1.262
f_bond_d
0.007
f_plane_restr
0.006
f_chiral_restr
0.167
f_dihedral_angle_d
16.957
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2492
Nucleic Acid Atoms
0
Heterogen Atoms
181
Solvent Atoms
273
Software
Software
Software Name
Purpose
DNA
data collection
MOLREP
phasing
PHENIX
refinement version: (phenix.refine: 1.8_1069)
XDS
data reduction
XDS
data scaling