2QGR | pdb_00002qgr

Structure of the R178A mutant of delta PDZ DegS protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QF0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	293	50 mM NaCacodylate pH 6.5, 100 mM NaCitrate, 20% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.216	α = 90
b = 70.216	β = 90
c = 119.228	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	123	IMAGE PLATE	RIGAKU RAXIS IV	Varimax-HR	2007-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	50	98.2				5938

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	2.7	2.8	87.5		0.201

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2QF0	2.7	29.46	5394	313	89.3	0.249	0.26	0.262	92.57

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]
-30.396			-30.396		60.792

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.01
f_bond_d	0.002
f_bond_d_na
f_bond_d_prot
f_angle_d
f_angle_d_na
f_angle_d_prot
f_angle_deg
f_angle_deg_na
f_angle_deg_prot
f_dihedral_angle_d_na
f_dihedral_angle_d_prot
f_improper_angle_d
f_improper_angle_d_na
f_improper_angle_d_prot
f_mcbond_it
f_mcangle_it
f_scbond_it
f_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
DENZO	data reduction