3D4R | pdb_00003d4r

CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			277	21.5% polyethylene glycol 3350, 0.214M ammonium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.877	α = 90
b = 109.858	β = 90
c = 135.8	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 325 mm CCD	FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR	2008-03-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929,0.97913	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	28.94	100				68137

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	2.2	2.26	100		0.612	1.1

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	2.2	28.94	68065	3446	100	0.195	0.193	0.19	0.236	0.24	30.66

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]
0.11			0.09		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.231
r_dihedral_angle_4_deg	18.763
r_dihedral_angle_3_deg	12.17
r_dihedral_angle_1_deg	3.898
r_scangle_it	2.787
r_scbond_it	1.961
r_angle_refined_deg	1.781
r_mcangle_it	1.315
r_angle_other_deg	0.951
r_mcbond_it	0.841
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.201
r_symmetry_vdw_other	0.197
r_nbd_other	0.193
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.166
r_mcbond_other	0.162
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.102
r_nbtor_other	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7362
Nucleic Acid Atoms
Solvent Atoms	532
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing