3IB2 | pdb_00003ib2

structure of the complex of C-terminal half (C-lobe) of bovine lactoferrin with alpha-methyl-4-(2-methylpropyl) benzene acetic acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.01M ZNSO4, 0.1M MES, 25% PEG, MONOMETHYL ETHER 550, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.319	α = 90
b = 50.48	β = 107.75
c = 66.116	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	300	IMAGE PLATE	MARRESEARCH	MIRROR	2007-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.29	20	89	0.125	0.064				15854

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	2.29	2.38	90.2		0.477	1.9

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	PDB ENTRY 2DWA	2.29	20	15841	15027	814	87.3	0.168	0.165	0.17	0.22	0.22	RANDOM	32.53

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]
-0.02		-0.95	-0.9		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.422
r_dihedral_angle_3_deg	20.348
r_dihedral_angle_4_deg	18.321
r_dihedral_angle_1_deg	7.914
r_scangle_it	5.175
r_scbond_it	3.255
r_mcangle_it	2.191
r_angle_refined_deg	1.71
r_mcbond_it	1.325
r_symmetry_hbond_refined	0.654
r_symmetry_metal_ion_refined	0.457
r_symmetry_vdw_refined	0.349
r_nbtor_refined	0.314
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.136
r_metal_ion_refined	0.135
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	122

Software

Software
Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling