6WFH | pdb_00006wfh

Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	25 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.7 M ammonium sulfate, 5% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.302	α = 90
b = 68.302	β = 90
c = 103.462	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	RAYONIX MX300HE	MD2 Micro Diffractometer	2020-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.84	30	99.9	0.12	0.12	0.126	0.035	9	13.2		21795		-3

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	1.85	1.92	100		1.103	1.103	2.632	13.5

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	1JC5	1.84	29.31	20711	1029	99.48	0.1653	0.1643	0.173	0.1863	0.1968	RANDOM	37.613

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			0.92		-1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.109
r_dihedral_angle_4_deg	13.736
r_dihedral_angle_3_deg	13.573
r_dihedral_angle_1_deg	7.482
r_angle_refined_deg	2.133
r_angle_other_deg	1.557
r_chiral_restr	0.27
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1075
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
ARP/wARP	model building
PHASER	phasing
HKL-2000	data reduction