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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
1Q3A
Crystal structure of the catalytic domain of human matrix metalloproteinase 10
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)
Biological Assembly 2 (gz) (A)
Biological Assembly 3 (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop
pH
8
Temperature
293.0
Details
Tris-HCl, PEG 6000, Acetohydroxamic acid, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 117.15
α = 90
b = 61.14
β = 108.68
c = 68.59
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 4
Si(111)
2003-04-04
Diffraction Radiation
Monochromator
Protocol
Si(111)
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID29
0.9330
ESRF
ID29
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
2.1
20
--
0.14
0.14
--
3.0
--
25246
0.0
0.0
--
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)
2.1
2.21
89.1
0.38
0.38
1.8
2.1
--
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
2.1
51.3
--
--
--
21809
1962
100.0
--
0.27785
0.27599
0.29797
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
2.1
2.155
--
108
1386
0.349
0.343
--
--
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
RESTRAINED
Mean Isotropic B
37.771
Anisotropic B[1][1]
-2.75
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-0.38
Anisotropic B[2][2]
0.87
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
1.63
RMS Deviations
Key
Refinement Restraint Deviation
r_scangle_it
2.328
r_nbd_refined
0.297
r_dihedral_angle_1_deg
10.558
r_symmetry_vdw_refined
0.362
r_xyhbond_nbd_refined
0.252
r_scbond_it
1.408
r_mcangle_it
1.251
r_angle_refined_deg
2.247
r_bond_refined_d
0.024
r_gen_planes_refined
0.009
r_metal_ion_refined
0.165
r_mcbond_it
0.656
r_symmetry_hbond_refined
0.241
r_chiral_restr
0.199
Coordinate Error
Parameter
Value
Luzzati ESD (R-Free Set)
0.33
Luzzati Sigma A (R-Free Set)
0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
3746
Nucleic Acid Atoms
0
Heterogen Atoms
78
Solvent Atoms
351
Software
Software
Software Name
Purpose
MOSFLM
data reduction
SCALA
data scaling
MOLREP
phasing
CNS
refinement
CCP4
data scaling version: (SCALA)
REFMAC
refinement version: 5.1.24