3NOJ | pdb_00003noj

The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	10% PEG 4000, 0.1 M Na acetate, 10 mM MgCl2, 5 mM pyruvate, 21 mg/ml protein, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.18	α = 90
b = 111.18	β = 90
c = 139.273	γ = 120

Symmetry
Space Group	H 3 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	RAYONIX MX-225	DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR	2009-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97950	CLSI	08ID-1

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	1.82	40	90.8	0.099	12	6.7	27093	27093	-3	-3

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	1.82	1.85	89.4		0.273	4.4	2.8

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 1NXJ	1.82	28.22	27093	25671	1421	90.84	0.15942	0.15879	0.17	0.17079	0.18	RANDOM	40.182

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]
-0.84	-0.42		-0.84		1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.591
r_dihedral_angle_4_deg	18.391
r_dihedral_angle_3_deg	11.302
r_dihedral_angle_1_deg	6.257
r_scangle_it	1.354
r_angle_refined_deg	1.046
r_scbond_it	0.894
r_angle_other_deg	0.821
r_mcangle_it	0.486
r_mcbond_it	0.412
r_symmetry_vdw_other	0.218
r_nbd_refined	0.201
r_nbd_other	0.186
r_nbtor_refined	0.159
r_symmetry_vdw_refined	0.159
r_symmetry_hbond_refined	0.127
r_xyhbond_nbd_refined	0.09
r_nbtor_other	0.08
r_mcbond_other	0.078
r_chiral_restr	0.059
r_metal_ion_refined	0.014
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1760
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	33

Software

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