5UJC | pdb_00005ujc

Crystal structure of a C.elegans B12-trafficking protein CblC, a human MMACHC homologue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SBZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	21.5% PEG 3350, 40 mM Spermidine-HCl, 0.2 M (NH4)2tartarate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.008	α = 90
b = 66.089	β = 90
c = 92.826	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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2014-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03325	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	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	1.35	53.84	92.9	0.054	0.062	0.029	0.997	15	3.8		66799			12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37	58.7		0.573	0.722	0.435	0.618	1.9	2.3

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	3SBZ	1.35	53.84	63476	3285	92.28	0.13361	0.13209	0.13	0.16303	0.17	RANDOM	18.25

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]
-0.92			1.79		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.461
r_sphericity_bonded	13.967
r_dihedral_angle_4_deg	12.944
r_dihedral_angle_3_deg	11.867
r_dihedral_angle_1_deg	5.93
r_long_range_B_refined	3.992
r_long_range_B_other	3.615
r_scangle_other	3.447
r_scbond_it	2.902
r_scbond_other	2.902
r_mcangle_it	2.713
r_mcangle_other	2.713
r_rigid_bond_restr	2.233
r_mcbond_other	2.195
r_mcbond_it	2.194
r_angle_refined_deg	2.013
r_angle_other_deg	0.736
r_chiral_restr	0.541
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003
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_scangle_it
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2184
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	128

Software

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