4COZ | pdb_00004coz

Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Galb1-3GlcNAc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AF9	PRUNED VERSION OF PDB ENTRY 4AF9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.08 M SODIUM ACETATE PH4.6, 1.6 M AMMONIUM SULFATE, 20% GLYCEROL, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALB1-3GLCNAC

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.28	α = 90
b = 61.26	β = 90
c = 106.62	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	PIXEL	DECTRIS PILATUS 6M		2012-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)		PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.25	53.12	99.9	0.17	12.1	9		13420		-3

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	2.25	2.37	100		0.65	3.5	9.2

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	PRUNED VERSION OF PDB ENTRY 4AF9	2.3	53.17	11930	624	99.75	0.17994	0.17779	0.1822	0.22029	0.2263	RANDOM	23.917

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]
0.28			0.57		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.772
r_dihedral_angle_3_deg	13.89
r_dihedral_angle_4_deg	10.466
r_dihedral_angle_1_deg	6.11
r_mcangle_it	1.706
r_angle_refined_deg	1.265
r_mcbond_it	0.903
r_mcbond_other	0.9
r_angle_other_deg	0.783
r_scbond_it	0.557
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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_it
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	1791
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	37

Software

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