2B65 | pdb_00002b65

Crystal structure of the complex of C-lobe of bovine lactoferrin with maltose at 1.5A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	0.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE, pH 6.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.484	α = 90
b = 49.846	β = 107.07
c = 65.161	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	203	CCD	MARRESEARCH	MIRROR	2005-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	0.803	EMBL/DESY, HAMBURG	X31

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	1.5	20	90.4	0.065	10		60932	60932			17.84

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	1.5	1.53	99.3		0.484	2.2

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1NKX	1.5	20	53616	1104	90.35	0.1961	0.194	0.1934	0.21862	RANDOM	21.556

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]
1.11		-0.51	-0.92		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.814
r_dihedral_angle_4_deg	17.404
r_dihedral_angle_3_deg	16.999
r_dihedral_angle_1_deg	7.422
r_scangle_it	4.868
r_scbond_it	3.556
r_mcangle_it	2.442
r_mcbond_it	2.238
r_angle_refined_deg	1.744
r_angle_other_deg	0.97
r_mcbond_other	0.535
r_symmetry_vdw_other	0.3
r_nbd_other	0.236
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.213
r_symmetry_vdw_refined	0.206
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.17
r_nbtor_other	0.115
r_chiral_restr	0.11
r_symmetry_metal_ion_refined	0.099
r_metal_ion_refined	0.057
r_xyhbond_nbd_other	0.015
r_gen_planes_refined	0.014
r_bond_refined_d	0.012
r_bond_other_d	0.007
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	435
Heterogen Atoms	202

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing