3MMG | pdb_00003mmg

Crystal structure of tobacco vein mottling virus protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q31	PDB entry 1Q31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.2M potassium formate 20% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.476	α = 90
b = 77.563	β = 90
c = 78.463	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	MARMOSAIC 300 mm CCD		2007-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97939	APS	22-ID

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	1.7	35	96.1	0.08	17.4	5.2	50064	50064

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)
	1.7	1.76	92.7		0.431	2.7	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1Q31	1.7	35	47451	2544	96.15	0.17634	0.17456	0.1737	0.20961	0.209	RANDOM	19.435

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]
1.02			-0.08		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.621
r_dihedral_angle_4_deg	15.813
r_dihedral_angle_3_deg	12.845
r_dihedral_angle_1_deg	6.685
r_scangle_it	3.615
r_scbond_it	2.307
r_mcangle_it	1.519
r_angle_refined_deg	1.335
r_mcbond_it	0.95
r_nbtor_refined	0.305
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3540
Nucleic Acid Atoms
Solvent Atoms	553
Heterogen Atoms	3

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling