3ELV | pdb_00003elv

Crystal Structure of Full-Length Yeast Pml1p

X-RAY DIFFRACTION

---

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
2.22	44.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.891	α = 90
b = 86.891	β = 90
c = 96.697	γ = 120

Symmetry
Space Group	P 32 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	100	CCD	MARMOSAIC 225 mm CCD	mirrors	2006-05-05	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	2.4	40.7	99.9	0.083	19.7	6.3	16912	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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.4	30	16064	16010	852	99.66	0.22027	0.22027	0.21798	0.26592	RANDOM	81.147

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]
-1.67	-0.84		-1.67		2.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.161
r_dihedral_angle_4_deg	18.873
r_dihedral_angle_3_deg	18.268
r_dihedral_angle_1_deg	6.186
r_scangle_it	1.697
r_angle_refined_deg	1.227
r_scbond_it	1.039
r_mcangle_it	0.923
r_mcbond_it	0.53
r_nbtor_refined	0.3
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.14
r_chiral_restr	0.091
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	15

Software

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