2R25 | pdb_00002r25

Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QSP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	295	2.2 M ammonium sulfate, 50 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.60

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.013	α = 90
b = 75.544	β = 90
c = 98.392	γ = 90

Symmetry
Space Group	P 21 21 21

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		2007-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B		NSLS	X12B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	50	97.9	0.048	28.8	6.1		51329

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.72	99.6		0.39		4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1QSP	1.7	17.75	43353	42989	2168	99.2	0.199	0.196	0.23	0.24	0.26	RANDOM	38.16

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]
0.01					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.153
r_dihedral_angle_3_deg	17.986
r_dihedral_angle_4_deg	17.835
r_dihedral_angle_1_deg	7.905
r_scangle_it	6.306
r_scbond_it	4.564
r_mcangle_it	3.995
r_mcbond_it	2.793
r_angle_refined_deg	2.565
r_metal_ion_refined	0.445
r_nbtor_refined	0.311
r_nbd_refined	0.26
r_symmetry_vdw_refined	0.253
r_chiral_restr	0.252
r_xyhbond_nbd_refined	0.203
r_symmetry_hbond_refined	0.142
r_bond_refined_d	0.032
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
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	2479
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling