6XEW | pdb_00006xew

Structure of Serratia marcescens 2,3-butanediol dehydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NI5

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
2.31	43.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.171	α = 90
b = 108.171	β = 90
c = 82.881	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	2017-03-23	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	2	50	100	0.1377	11.23	11.42		33823

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	2	2.1	100		0.6889	1.96	8.77

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4NI5	2	45.335	33602	1711	99.503	0.165	0.1622	0.17	0.2141	0.22	24.025

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]
-0.405			-0.405		0.809

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.346
r_dihedral_angle_4_deg	19.048
r_dihedral_angle_3_deg	13.582
r_dihedral_angle_1_deg	7.462
r_lrange_it	5.646
r_lrange_other	5.478
r_scangle_it	4.011
r_scangle_other	4.011
r_mcangle_it	2.684
r_mcangle_other	2.684
r_scbond_it	2.586
r_scbond_other	2.585
r_mcbond_it	1.847
r_mcbond_other	1.846
r_angle_refined_deg	1.497
r_angle_other_deg	1.441
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.212
r_nbd_other	0.202
r_xyhbond_nbd_refined	0.189
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_other	0.112
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3661
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	127

Software

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