3SBY | pdb_00003sby

Crystal Structure of SeMet-Substituted Apo-MMACHC (1-244), a human B12 processing enzyme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	277	0.96 M sodium malonate, 10% Jeffamine 600 pH 7.0, 0.1 M Hepes 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.267	α = 90
b = 69.267	β = 90
c = 201.848	γ = 120

Symmetry
Space Group	P 65

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	2010-06-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97954	APS	23-ID-D

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	2.7	59.99	100	0.133	13.7	7.7	14979	14979

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	2.7	2.8	100		0.473		7.5	1491

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2.71	59.99	14932	14911	755	99.89	0.276	0.2314	0.2283	0.2352	0.2903	0.2918	RANDOM	42.6535

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]
0.57	0.28		0.57		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.855
r_dihedral_angle_3_deg	17.358
r_dihedral_angle_4_deg	14.514
r_dihedral_angle_1_deg	5.381
r_scangle_it	1.539
r_angle_refined_deg	1.052
r_scbond_it	0.925
r_mcangle_it	0.728
r_mcbond_it	0.383
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3615
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling