3MKM | pdb_00003mkm

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q8F	YEIK PDB CODE 1Q8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	25% PEG 3350, 0.1M TRIS PH 8.5, 0.2M SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.601	α = 66.65
b = 85.231	β = 79.39
c = 90.06	γ = 85.3

Symmetry
Space Group	P 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	ADSC QUANTUM 4		2005-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	2.2	81.65	94.8	0.112	0.112	10.8	3.3		58257

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)
	2.2	2.32	94.5		0.363	0.363	3.2	3.2

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	YEIK PDB CODE 1Q8F	2.2	47.91	55302	2954	94.43	0.18687	0.18494	0.19	0.22284	0.23	RANDOM	24.962

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]
1.11	0.59	1.31	-1.2	0.04	-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_3_deg	13.953
r_dihedral_angle_4_deg	10.723
r_dihedral_angle_1_deg	6.11
r_scangle_it	1.816
r_angle_refined_deg	1.321
r_scbond_it	1.267
r_angle_other_deg	1.101
r_mcangle_it	0.696
r_mcbond_it	0.457
r_symmetry_vdw_other	0.281
r_symmetry_vdw_refined	0.218
r_symmetry_hbond_refined	0.212
r_nbd_refined	0.204
r_nbd_other	0.187
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.167
r_mcbond_other	0.129
r_nbtor_other	0.086
r_chiral_restr	0.081
r_metal_ion_refined	0.07
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	9129
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling