2BB6 | pdb_00002bb6

Structure of Cobalamin-complexed Bovine Transcobalamin in Monoclinic Crystal Form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		UNREFINED PARTIAL MODEL FROM PHASING WITH SHARP V2.0 USING SINGLE-WAVELENGTH ANOMALOUS DISPERSION DATA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	293	28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.826	α = 90
b = 100.664	β = 97.16
c = 99.143	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	100	CCD	MARRESEARCH		2002-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R		ELETTRA	5.2R

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	18	96.8	0.097	0.097	12	3.5		121830			25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	93.3		0.522	0.522	2.2	3.2

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	UNREFINED PARTIAL MODEL FROM PHASING WITH SHARP V2.0 USING SINGLE-WAVELENGTH ANOMALOUS DISPERSION DATA	2	18	116949	116949	4895	96.8	0.243	0.241	0.25	0.28	0.28	RANDOM	32.24

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]
0.79		0.27	-1.06		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.024
r_dihedral_angle_4_deg	23.697
r_dihedral_angle_3_deg	20.727
r_dihedral_angle_1_deg	6.996
r_scangle_it	3.192
r_scbond_it	1.953
r_mcangle_it	1.489
r_angle_refined_deg	1.355
r_mcbond_it	0.789
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13016
Nucleic Acid Atoms
Solvent Atoms	764
Heterogen Atoms	368

Software

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