4CPB | pdb_00004cpb

CRYSTAL STRUCTURE OF LECA IN COMPLEX WITH A DIVALENT GALACTOSIDE AT 1. 57 ANGSTROM IN MAGNESIUM

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		SOLUTION 15 OF THE CSSI SCREEN 10 % PEG 8K, 10% PEG 1K, 100 MM TRIS 8.5 AND 200 MM MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.666	α = 90
b = 65.393	β = 90
c = 159.869	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 CCD		2013-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.57	39.97	99.9	0.07	19.2	7.6		75110		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	1.57	1.6	99.4		0.38	2.9	4

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 1OKO	1.57	39.97	71247	3777	99.85	0.16471	0.16331	0.18	0.19138	0.2	RANDOM	35.32

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]
-0.97			2.72		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.155
r_dihedral_angle_3_deg	11.919
r_dihedral_angle_4_deg	6.78
r_dihedral_angle_1_deg	5.9
r_scbond_it	2.219
r_mcangle_it	1.89
r_angle_refined_deg	1.763
r_mcbond_it	1.339
r_mcbond_other	1.337
r_angle_other_deg	0.795
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.24
r_symmetry_vdw_other	0.214
r_nbtor_refined	0.178
r_nbd_other	0.177
r_metal_ion_refined	0.115
r_chiral_restr	0.105
r_xyhbond_nbd_refined	0.104
r_nbtor_other	0.081
r_symmetry_hbond_refined	0.039
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_xyhbond_nbd_other	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_other
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	3619
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	142

Software

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