3NXF | pdb_00003nxf

Robust computational design, optimization, and structural characterization of retroaldol enzymes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A53	PDB ENTRY 1A53, with design and adjacent residues pared to alanine

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Protein at 5mg/ml in 100mm NaCl, 25mm Tris pH 7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mm Na acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.916	α = 90
b = 61.916	β = 90
c = 121.241	γ = 120

Symmetry
Space Group	P 31 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	93	CCD	RIGAKU SATURN 944+	Varimax HF	2009-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.09	53.61	99.4	14.9	3.8	11053	10320		2	46.1

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	2.09	2.16	99.9		0.7	2.07	3.1	1615

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1A53, with design and adjacent residues pared to alanine	2.4	53.61	2	11023	10320	522	98.22	0.22672	0.22672	0.22454	0.23	0.26821	0.27	RANDOM	48.845

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]
1.4	0.7		1.4		-2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.523
r_dihedral_angle_3_deg	17.172
r_dihedral_angle_4_deg	13.289
r_dihedral_angle_1_deg	6.527
r_scangle_it	3.635
r_scbond_it	2.326
r_mcangle_it	1.797
r_angle_refined_deg	1.375
r_mcbond_it	1.011
r_nbtor_refined	0.305
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.207
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2000
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	5

Software

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