3NQ2

Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R2 3/5G

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	277	PCB pH5.0, PEG 1500, pH 5.5, Microbatch, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.008	α = 90
b = 96.228	β = 125.88
c = 71.274	γ = 90

Symmetry
Space Group	C 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		IMAGE PLATE	RIGAKU RAXIS IV++	mirror	2008-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.02	50	97.9	0.07	0.051	19.6	5.1	35683	34934			19.24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.09	95.3		0.32	0.282	3.07	4.4	3420

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3NPU	2.02	50	33171	1757	97.85	0.20806	0.20521	0.26019	RANDOM	19.241

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]
-0.39		-0.4	-0.28		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.822
r_dihedral_angle_4_deg	14.889
r_dihedral_angle_3_deg	13.968
r_dihedral_angle_1_deg	6.211
r_scangle_it	3.648
r_scbond_it	2.326
r_angle_refined_deg	1.338
r_mcangle_it	1.304
r_mcbond_it	0.856
r_angle_other_deg	0.618
r_nbd_other	0.505
r_nbtor_refined	0.293
r_symmetry_vdw_refined	0.239
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.093
r_symmetry_hbond_refined	0.065
r_bond_refined_d	0.016
r_bond_other_d	0.014
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
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	3640
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	10

Software

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