3K6Z | pdb_00003k6z

Crystal structure of Rv3671c protease, inactive form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K6Y	PDB entry 3K6Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	Reservoir: 0.1 M Tris-HCl pH 8.5, 2.1 M ammonium phosphate monobasic, 60 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.074	α = 90
b = 43.693	β = 104.76
c = 71.468	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 300 mm CCD		2009-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12719	APS	21-ID-D

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	1.75	50	96.5	0.056		6.9	34080	32887	3	3

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)
	1.75	1.81	69.9		0.315	3.4	4.1	3564

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 (All)	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 3K6Y	1.75	40	34129	32887	1745	96.36	0.19024	0.19024	0.18773	0.1898	0.23903	0.2357	RANDOM	19.587

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]
0.36		-0.3	0.29		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.714
r_dihedral_angle_4_deg	13.95
r_dihedral_angle_3_deg	12.916
r_dihedral_angle_1_deg	5.856
r_scangle_it	2.597
r_scbond_it	1.673
r_angle_refined_deg	1.184
r_mcangle_it	0.973
r_mcbond_it	0.727
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.281
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.162
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling