2YXB | pdb_00002yxb

Crystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	oil batch		293	0.4M Ammonium dihydrogen phosphate, oil batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.662207	26.00201

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.902	α = 90
b = 51.134	β = 90
c = 54.564	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	RIGAKU JUPITER 210	mirrors	2006-10-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.97884, 0.90000, 0.97938	SPring-8	BL26B2

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	1.8	50	99.8	0.067	17.8	6.6		11582		-3

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	1.8	1.86	98.9		0.35	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.8	37.27	10970	552	99.56	0.21373	0.21194	0.2221	0.24713	0.2488	RANDOM	33.745

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			0.52		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	6.835
r_dihedral_angle_1_deg	6.365
r_scbond_it	4.419
r_mcangle_it	2.888
r_angle_refined_deg	2.166
r_mcbond_it	1.633
r_angle_other_deg	1.002
r_nbd_other	0.255
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.222
r_symmetry_vdw_other	0.219
r_symmetry_hbond_refined	0.204
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.148
r_nbtor_other	0.092
r_bond_refined_d	0.033
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	1074
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing