3DQG | pdb_00003dqg

Peptide-binding domain of heat shock 70 kDa protein F, mitochondrial precursor, from Caenorhabditis elegans.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OP6	2OP6.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	0.2 M ammonium sulfate, 20% PEG-4000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.418	α = 90
b = 120.159	β = 90
c = 56.77	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	ADSC QUANTUM 315		2007-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-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	1.72	37.6	95.6	0.061	11.4	6.6	63652	63652			29.6

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	1.72	1.76	64.3		0.551	1.92	3.9	2798

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2OP6.pdb	1.72	37.5	63579	63579	3230	95.5	0.184	0.184	0.183	0.181	0.216	0.2151	RANDOM	17.35

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]
-1.26			-1.13		2.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.903
r_dihedral_angle_4_deg	16.226
r_dihedral_angle_3_deg	15.81
r_dihedral_angle_1_deg	5.8
r_scangle_it	4.034
r_scbond_it	2.474
r_angle_refined_deg	1.575
r_mcangle_it	1.373
r_mcbond_it	0.965
r_nbtor_refined	0.303
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.203
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.116
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4387
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection