1NMP | pdb_00001nmp

Structural genomics, ybgI protein, unknown function

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SeMet structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M cacodylate buffer pH 7.5, 0.1M magnesium acetate, 15% (w/v) polyethylene glycol 8000, 5% (v/v) polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.73	α = 90
b = 156.73	β = 90
c = 57.61	γ = 120

Symmetry
Space Group	P 3

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	MARRESEARCH		2002-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9793	APS	22-ID

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	2.2	20		0.096	14.1	5		80094			4.1

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	SeMet structure	2.2	19.76	80007	4000	95.9	0.212	0.212	0.21	0.253	0.25	RANDOM	13.6

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]
2.19	2.53		2.19		-4.39

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.2
c_scangle_it	2.58
c_angle_deg	2.2
c_scbond_it	1.9
c_mcangle_it	1.52
c_improper_angle_d	1.4
c_mcbond_it	1.07
c_bond_d	0.026
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11382
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	11

Software

Software
Software Name	Purpose
MAR345	data collection
d*TREK	data reduction
CNS	refinement
d*TREK	data scaling
CNS	phasing