3IIO

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IIV	PDB ENTRY 3IIV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	8.5	292	0.2M NaF, 0.1M Bis Tris, pH8.5, 20% PEG3350, Microbatch under oil, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.584	α = 90
b = 106.584	β = 90
c = 128.753	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2007-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.954	ESRF	BM14

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	2.25	50	99.1			77187	77888	330399

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.33	95.7

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 3IIV	2.25	50	73916	73236	3874	99.08	0.21771	0.21455	0.21	0.27758	0.28	RANDOM	34.855

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]
0.18	0.09		0.18		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.465
r_dihedral_angle_4_deg	21.481
r_dihedral_angle_3_deg	17.723
r_dihedral_angle_1_deg	6.207
r_angle_refined_deg	1.525
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11630
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms

Software

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