4PVC | pdb_00004pvc

Crystal structure of yeast methylglyoxal/ isovaleraldehyde reductase Gre2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y1P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	289	25% polyethylene glycol 2000 mmE, 0.2M (NH4)2SO4, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.721	α = 90
b = 97.845	β = 90
c = 139.003	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	ADSC QUANTUM 315r		2009-12-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9701	SSRF	BL17U

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	50	99.2	0.079	0.079	18.07	4.5		45207		-3

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	2.03	97.1		0.207	0.207	6.323	4	2208

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1Y1P	2	50	45207	42922	2285	98.77	0.22612	0.22401	0.2241	0.26593	0.2656	RANDOM	56.934

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]
-1.87			0.15		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.308
r_dihedral_angle_4_deg	16.369
r_dihedral_angle_3_deg	14.12
r_dihedral_angle_1_deg	5.26
r_scangle_it	2.495
r_mcangle_it	1.902
r_scbond_it	1.423
r_mcbond_it	1.133
r_angle_refined_deg	1.044
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5380
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling