2PGC | pdb_00002pgc

Crystal structure of a a marine metagenome protein (jcvi_pep_1096685590403) from uncultured marine organism at 2.53 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	277	NANODROP, 0.2M K2SO4, 20.0% PEG 3350, No Buffer pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.475	α = 90
b = 139.935	β = 90
c = 60.785	γ = 90

Symmetry
Space Group	P 21 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	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-03-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97949	SSRL	BL11-1

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	2.53	29.921	99.8	0.076	0.076	7.7	3.6		39917			62.23

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	2.53	2.6	99.6		0.684	0.684	1.1	3.6	2884

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 (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	MAD	THROUGHOUT	2.53	29.921	39877	2000	99.72	0.215	0.215	0.214	0.216	0.246	0.2439	RANDOM	53.528

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]
0.31			-0.71		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.652
r_dihedral_angle_4_deg	21.959
r_dihedral_angle_3_deg	16.081
r_scangle_it	5.075
r_dihedral_angle_1_deg	5.042
r_scbond_it	4.023
r_mcangle_it	2.366
r_mcbond_it	1.492
r_angle_refined_deg	1.246
r_angle_other_deg	0.867
r_mcbond_other	0.45
r_symmetry_vdw_other	0.255
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.199
r_nbd_other	0.184
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_refined	0.139
r_nbtor_other	0.086
r_chiral_restr	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_xyhbond_nbd_other	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7857
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing