3DEP | pdb_00003dep

Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DEO	PDB ID 3DEO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.473	α = 90
b = 66.473	β = 90
c = 219.703	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	ADSC QUANTUM 4		2007-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.9310	ESRF	ID14-3

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	2.7	35	99.1	0.103	0.103	3.6	6.5	10129	8435

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)
	2.7	2.85	99.6		0.451	0.451	3.6	6.8	1193

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	PDB ID 3DEO	2.7	35	8434	397	98.41	0.252	0.249	0.2481	0.298	0.2945	RANDOM	67.743

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]
-3.3	-1.65		-3.3		4.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.779
r_dihedral_angle_3_deg	19.128
r_dihedral_angle_4_deg	18.746
r_dihedral_angle_1_deg	6.787
r_scangle_it	2.493
r_scbond_it	1.561
r_angle_refined_deg	1.452
r_mcangle_it	1.314
r_mcbond_it	0.776
r_nbtor_refined	0.314
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.205
r_symmetry_vdw_refined	0.173
r_chiral_restr	0.107
r_symmetry_hbond_refined	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1492
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection