1IPF | pdb_00001ipf

TROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AE2	PDB ENTRY 2AE2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	lithium sulfate, dithiothreitol, HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.6	α = 90
b = 88.6	β = 90
c = 337.2	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	288	IMAGE PLATE	FUJI		1998-12-11	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.7-1.65	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	37	86.5	0.134		6.34	24958	24567		1	12.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	84.3		0.27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 2AE2	2.5	10	2	23323	1193	84.1	0.197	0.1907	0.265	0.2552	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	23.81
x_angle_deg	1.33
x_improper_angle_d	0.685
x_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3950
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	116

Software

Software
Software Name	Purpose
INTLAUE	data collection
LAUENORM	data reduction
X-PLOR	model building
X-PLOR	refinement
INTLAUE	data reduction
LAUENORM	data scaling
X-PLOR	phasing