7A2B | pdb_00007a2b

X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q207D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6H07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	Protein solution (10 g/L LbADH, 20mM HEPES/NaOH pH7.0, 1 mM MgCl2) and precipitation buffer (1 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 100 g/L PEG 550 MME)

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.82	α = 90
b = 80.52	β = 90
c = 115.1	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	DECTRIS PILATUS 2M-F		2019-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.399	46.83	99.6	0.05	0.999	17.4	4.07		98425

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.49	98.6		0.174	0.9969	5.43	3.91

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	6h07	1.399	40.26	51330	2567	99.724	0.146	0.144	0.14	0.175	0.17	16.542

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]
-0.977			2.31		-1.333

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.087
r_dihedral_angle_4_deg	20.013
r_dihedral_angle_3_deg	11.555
r_dihedral_angle_1_deg	6.5
r_lrange_it	2.277
r_lrange_other	2.072
r_scangle_it	1.788
r_scangle_other	1.788
r_mcangle_it	1.478
r_mcangle_other	1.478
r_angle_other_deg	1.401
r_scbond_it	1.378
r_scbond_other	1.378
r_angle_refined_deg	1.29
r_mcbond_it	1.223
r_mcbond_other	1.223
r_rigid_bond_restr	0.959
r_nbd_refined	0.208
r_nbd_other	0.206
r_symmetry_nbd_refined	0.197
r_symmetry_nbd_other	0.166
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1870
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing