2NVN | pdb_00002nvn

Crystal structure of a protein with a cupin-like fold and unknown function (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	277	2.5M NaCl, 0.1M Imidazole, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
5.02	75.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.18	α = 90
b = 82.18	β = 90
c = 80.5	γ = 90

Symmetry
Space Group	P 43 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	ADSC QUANTUM 315	FIXED-HEIGHT EXIT BEAM, TOROIDAL FOCUSING MIRROR	2006-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2		ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	29.05	99.4	0.059	13.56	6.88		10011			71.4

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	2.5	2.59	97.7		0.797	1.63

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	SAD	THROUGHOUT	2.5	29.05	9972	478	99.8	0.209	0.208	0.21	0.227	0.24	RANDOM	26.66

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]
-1.14			-1.14		2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.169
r_dihedral_angle_4_deg	16.381
r_dihedral_angle_3_deg	15.189
r_dihedral_angle_1_deg	5.126
r_scangle_it	2.653
r_angle_refined_deg	1.823
r_scbond_it	1.748
r_angle_other_deg	1.479
r_mcangle_it	1.131
r_mcbond_it	0.863
r_symmetry_vdw_other	0.216
r_nbd_refined	0.181
r_nbtor_refined	0.162
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.138
r_mcbond_other	0.136
r_chiral_restr	0.108
r_symmetry_vdw_refined	0.098
r_symmetry_hbond_refined	0.081
r_nbtor_other	0.079
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
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	930
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing