2OW2 | pdb_00002ow2

MMP-9 active site mutant with difluoro butanoic acid inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GKD	PDB ENTRY 1GKD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4	293	3.0 M NaCl, 0.1 M citric acid, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K, pH 4.0, pH 4.00

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.42	α = 90
b = 55.42	β = 90
c = 260.793	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm	MIRRORS	2006-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.82	20	93.7	0.122	12.4			9963		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.82	2.87	77.8		0.475	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GKD	2.9	19.73	8803	8803	474	90.4	0.215	0.215	0.2	0.285	0.28	RANDOM	40.9

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
10.6			10.6		-21.21

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.5
c_scangle_it	2.55
c_mcangle_it	2.03
c_scbond_it	1.57
c_mcbond_it	1.18
c_angle_deg	1
c_improper_angle_d	0.73
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2486
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	50

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing