1NXQ | pdb_00001nxq

Crystal Structure of R-alcohol dehydrogenase (RADH) (apoenyzme) from Lactobacillus brevis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HSD	PDB FILE 2HSD REDUCED TO A POLY-ALA CHAIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	40%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.444	α = 90
b = 85.065	β = 90
c = 115.336	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	283	IMAGE PLATE	MACSCIENCE		1997-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.5418

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	1.79	68.5	98.9	0.059	46.4	9.5	26474	26183			14.5

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	1.79	1.86	91.3		0.235	11.2	8.3

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-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 FILE 2HSD REDUCED TO A POLY-ALA CHAIN	1.79	69.01	25103	1079	99.16	0.15112	0.15112	0.14997	0.16	0.17819	0.19	RANDOM	17.002

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]
-0.69			0.77		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	13.215
r_dihedral_angle_1_deg	3.955
r_scangle_it	3.569
r_scbond_it	2.12
r_mcangle_it	1.265
r_angle_refined_deg	1.233
r_angle_other_deg	1.165
r_mcbond_it	0.669
r_nbd_refined	0.228
r_symmetry_vdw_other	0.212
r_nbd_other	0.194
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.113
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1871
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing