2YIO | pdb_00002yio

Crystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with 1-Thio-beta-D-Galactose (SPACEGROUP C2221)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YIL	PDB ENTRY 2YIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	291	VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. PROTEIN SOLUTION:50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12 MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, 0.1 M NACL, 1.7 M AMMONIUM SULFATE, 15% GLYCEROL. DROPLET: 1 MICROLITER PROTEIN SOLUTION: 1 MICROLITER RESERVOIR SOLUTION. PROTEIN:1-THIO-BETA-D-GALACTOSE, MOLAR RATIO 1:100.

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.73	α = 90
b = 81.99	β = 90
c = 130.96	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MARRESEARCH MAR30	GOEBEL MIRROR	2000-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU H2B

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	2.43	23.9	99.1	0.04	29.1	5		15317		-3	30.2

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	2.43	2.5	92.6		0.15	8.44	3.9

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	PDB ENTRY 2YIL	2.43	23.83	14549	765	100	0.17267	0.17045	0.18	0.21379	0.22	RANDOM	36.229

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	31.992
r_dihedral_angle_3_deg	15.163
r_dihedral_angle_4_deg	13.126
r_dihedral_angle_1_deg	6.927
r_scangle_it	5.491
r_scbond_it	3.751
r_mcangle_it	2.382
r_angle_refined_deg	1.791
r_mcbond_it	1.307
r_angle_other_deg	0.969
r_mcbond_other	0.39
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1976
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing