9FTK | pdb_00009ftk

Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3 bound to substrate intermediate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8DO5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.4 M Ammonium phosphate monobasic

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.511	α = 90
b = 199.715	β = 92.581
c = 144.511	γ = 90

Symmetry
Space Group	I 1 2 1

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		2010-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0718	ESRF	ID23-1

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	1.76	46.7	90.5	0.107	0.994	6.2	2		366454

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	1.76	1.85	90.3		0.61	0.819		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.76	46.7	366310	18623	90.464	0.179	0.1773	0.19	0.2154	0.2253	15.659

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]
-0.002		0.136	0.335		-0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.2
r_dihedral_angle_3_deg	12.84
r_dihedral_angle_2_deg	12.211
r_dihedral_angle_1_deg	6.452
r_lrange_it	6.316
r_lrange_other	6.3
r_scangle_it	4.017
r_scangle_other	4.017
r_scbond_it	2.588
r_scbond_other	2.588
r_mcangle_other	2.039
r_mcangle_it	2.038
r_angle_refined_deg	1.766
r_mcbond_it	1.347
r_mcbond_other	1.346
r_angle_other_deg	1.068
r_chiral_restr_other	0.953
r_symmetry_nbd_refined	0.341
r_symmetry_xyhbond_nbd_refined	0.318
r_xyhbond_nbd_other	0.283
r_xyhbond_nbd_refined	0.263
r_symmetry_xyhbond_nbd_other	0.248
r_nbd_refined	0.231
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.184
r_nbd_other	0.178
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.084
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20262
Nucleic Acid Atoms
Solvent Atoms	3945
Heterogen Atoms	334

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing