3BIC

Crystal structure of human methylmalonyl-CoA mutase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1REQ	PDB entry 1REQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	1.60M Na/K2PO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.75	α = 90
b = 95.15	β = 108.31
c = 119.16	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	MARMOSAIC 225 mm CCD		2007-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97649	SLS	X10SA

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	2.6	37.42	99.6	0.122	0.122	9.5	3.6	67606	67606

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	2.6	2.74	97.3		0.698	0.698	1.6	2.8

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1REQ	2.6	37.42	66447	66447	1152	99.55	0.21758	0.21758	0.21712	0.24341	RANDOM	33.85

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]
1.08		2.7	-1.18		1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.51
r_dihedral_angle_4_deg	20.401
r_dihedral_angle_3_deg	14.96
r_dihedral_angle_1_deg	5.461
r_scangle_it	1.556
r_angle_refined_deg	1.121
r_angle_other_deg	0.949
r_scbond_it	0.947
r_mcangle_it	0.701
r_mcbond_it	0.415
r_nbd_refined	0.207
r_symmetry_vdw_other	0.207
r_symmetry_vdw_refined	0.192
r_nbd_other	0.178
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.113
r_nbtor_other	0.084
r_chiral_restr	0.061
r_mcbond_other	0.059
r_symmetry_hbond_refined	0.018
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10642
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing