3ELS | pdb_00003els

Crystal Structure of Yeast Pml1p, Residues 51-204

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100 mM Tris-HCl, pH 7.5, 200 mM Li2SO4, 21-24 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.613	α = 90
b = 100.613	β = 90
c = 102.196	γ = 120

Symmetry
Space Group	H 3 2

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	MARMOSAIC 225 mm CCD	mirrors	2007-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	0.9802	MPG/DESY, HAMBURG	BW6

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	1.8	40.7	99.9	0.083	19.7	6.3		16896			71.7

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	2.4	2.53	100		0.81	1.6	6.2	2473

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	30	17744	17665	949	99.55	0.19133	0.19133	0.18898	0.1902	0.23611	RANDOM	36.309

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]
-1.69	-0.84		-1.69		2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.653
r_dihedral_angle_4_deg	17.672
r_dihedral_angle_3_deg	12.925
r_dihedral_angle_1_deg	6.288
r_scangle_it	2.917
r_scbond_it	1.859
r_mcangle_it	1.308
r_angle_refined_deg	1.277
r_mcbond_it	0.826
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1168
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MAR345dtb	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling