3FR8 | pdb_00003fr8

rice Ketolacid reductoisomerase in complex with Mg2+-NADPH

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.1M TRIS-HCl pH 8.5, 1M (NH4)2SO4, 15% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.06	α = 90
b = 162.06	β = 90
c = 196.47	γ = 90

Symmetry
Space Group	I 41 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	CCD	RIGAKU SATURN 944	Osmic mirrors	2008-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.8	19.22	98	0.103	0.103		3.2	31711	31711

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	2.8	2.9	99.8		0.02	0.354	2	2.7	3170

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	PDB entry 1YVE	2.8	19.22	31711	29991	1598	97.71	0.23564	0.23307	0.2449	0.28398	0.2798	RANDOM	46.985

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]
0.06			0.06		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.609
r_dihedral_angle_3_deg	16.385
r_dihedral_angle_4_deg	14.361
r_dihedral_angle_1_deg	5.012
r_angle_refined_deg	1.046
r_scangle_it	0.709
r_scbond_it	0.408
r_mcangle_it	0.374
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.218
r_mcbond_it	0.211
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_refined	0.108
r_metal_ion_refined	0.108
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7815
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	112

Software

Software
Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
CrystalClear	data reduction
SCALEPACK	data scaling