3GWP | pdb_00003gwp

Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	277	0.2000M (NH4)2Tartrate, 20.0000% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.74	α = 90
b = 108.948	β = 90
c = 207.642	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	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	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
1	2.9	29.775	99.9	0.243	0.243	3.121	3.7		40426			42.549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	100		0.749	0.749	1	3.7	2934

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	MR	THROUGHOUT	3FD0	2.9	29.775	40367	2022	99.86	0.225	0.223	0.23	0.271	0.27	RANDOM	24.943

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]
-1.65			-0.4		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.6
r_dihedral_angle_3_deg	9.036
r_dihedral_angle_4_deg	8.808
r_dihedral_angle_1_deg	2.167
r_angle_refined_deg	1.065
r_angle_other_deg	0.879
r_mcangle_it	0.526
r_scangle_it	0.397
r_mcbond_it	0.318
r_scbond_it	0.26
r_symmetry_hbond_refined	0.17
r_nbtor_refined	0.164
r_nbd_refined	0.161
r_xyhbond_nbd_refined	0.157
r_nbd_other	0.139
r_symmetry_vdw_other	0.123
r_nbtor_other	0.084
r_symmetry_vdw_refined	0.079
r_chiral_restr	0.065
r_mcbond_other	0.061
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_xyhbond_nbd_other	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12883
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PHASER	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction