3UD6 | pdb_00003ud6

Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design

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, MODIFIED TO PREVENT MODEL BIAS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	298	Protein at 5mg/ml in 100mm NaCl, 25mm TRIS pH7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mN Na acetate pH5.5, vapor diffusion, temperature 298k, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.684	α = 90
b = 62.684	β = 90
c = 123.68	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	100	CCD	RIGAKU SATURN 944+	VARIMAX HF	2009-07-18	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)	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	2.091	50	99	0.037	22	2.9		17137		2	29.82

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	2.091	2.16	95.2		0.153	6.86	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1A53, MODIFIED TO PREVENT MODEL BIAS	2.091	19.47	16229	868	99.3	0.227	0.227	0.21	0.258	0.26	RANDOM	32.85

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]
-0.01	-0.01		-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.439
r_dihedral_angle_4_deg	16.778
r_dihedral_angle_3_deg	15.268
r_dihedral_angle_1_deg	4.933
r_scangle_it	3.215
r_scbond_it	1.908
r_mcangle_it	1.376
r_angle_refined_deg	1.028
r_mcbond_it	0.765
r_nbtor_refined	0.299
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	1995
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	27

Software

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