1VKH | pdb_00001vkh

CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		298	16.00% PEG MME 2000, 0.10M HEPES, 0.00M HEPES_Na, 5% Glycerol , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.93	35.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.967	α = 90
b = 85.959	β = 97.71
c = 70.479	γ = 90

Symmetry
Space Group	P 1 21 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		2003-11-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 8-BM	0.9464, 0.979326, 0.979179	APS	8-BM

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	1.85	50	99.77	0.069	17.88	3.89		42225			27.53

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	1.85	1.92	98.39		0.343	3.57	3.57	4159

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.85	37.44	39479	2060	100	0.14523	0.14292	0.15	0.1894	0.15	RANDOM	26.642

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]
-0.07		-0.02	0.07		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.422
r_dihedral_angle_4_deg	16.53
r_dihedral_angle_3_deg	13.328
r_dihedral_angle_1_deg	5.771
r_scangle_it	4.247
r_scbond_it	3.072
r_angle_refined_deg	1.698
r_mcangle_it	1.659
r_mcbond_it	1.496
r_angle_other_deg	0.909
r_mcbond_other	0.373
r_symmetry_vdw_other	0.266
r_symmetry_vdw_refined	0.245
r_symmetry_hbond_refined	0.237
r_nbd_refined	0.215
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.11
r_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4133
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
RESOLVE	phasing