6VSP | pdb_00006vsp

Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VSM	PDB entry 6VSM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M sodium malonate, pH 6-7, 6-15% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.675	α = 90
b = 108.675	β = 90
c = 82.948	γ = 90

Symmetry
Space Group	P 43 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	Bruker Platinum 135	HELIOS MIRRORS	2017-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	50	100	0.1087	18.67	17.32		39724

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2			0.7479	2.58

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 (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 6VSM	1.9	50	39547	1895	99.665	0.17	0.1677	0.2219	24.012

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]
-0.113			-0.113		0.226

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.734
r_dihedral_angle_4_deg	19.432
r_dihedral_angle_3_deg	13.587
r_dihedral_angle_1_deg	7.467
r_lrange_it	6.232
r_lrange_other	6.03
r_scangle_it	4.006
r_scangle_other	4.006
r_mcangle_other	2.878
r_mcangle_it	2.876
r_scbond_it	2.631
r_scbond_other	2.631
r_mcbond_it	1.968
r_mcbond_other	1.964
r_angle_refined_deg	1.486
r_angle_other_deg	1.404
r_symmetry_xyhbond_nbd_other	0.387
r_nbd_refined	0.228
r_nbd_other	0.204
r_xyhbond_nbd_refined	0.202
r_symmetry_nbd_refined	0.186
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.156
r_metal_ion_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.13
r_ncsr_local_group_1	0.118
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3668
Nucleic Acid Atoms
Solvent Atoms	539
Heterogen Atoms	151

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
PROTEUM PLUS	data reduction
PROTEUM PLUS	data collection