2NRA | pdb_00002nra

Crystal structure of Pi initiator protein in complex with iteron DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	294	5% polyethylene glycol 8000, 50 mM MgCl2 and 100 mM NH4H2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.9	α = 90
b = 125.9	β = 90
c = 138.2	γ = 120

Symmetry
Space Group	P 61 2 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 225 mm CCD		2005-02-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2005-05-08	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.076	APS	22-ID
2	SYNCHROTRON	NSLS BEAMLINE X12B	0.9201, 0.9208, 0.9184	NSLS	X12B

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	3.1	35.1	99.5	0.064	0.064	44.9	10	12173	12173			106.6

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	3.1	3.21	100		0.449	0.449	4.2	8.3	1193

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3.1	35.1	12161	12161	593	99.45	0.227	0.227	0.224	0.21	0.267	0.26	RANDOM	81.516

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]
-0.04	-0.02		-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.866
r_dihedral_angle_3_deg	23.672
r_dihedral_angle_4_deg	16.868
r_dihedral_angle_1_deg	8.708
r_scangle_it	2.193
r_angle_refined_deg	1.854
r_scbond_it	1.29
r_mcangle_it	1.199
r_mcbond_it	0.678
r_symmetry_hbond_refined	0.349
r_nbtor_refined	0.326
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.248
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.111
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2000
Nucleic Acid Atoms	936
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing