3BFK | pdb_00003bfk

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OIV	PDB entry 1OIV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.9	293	26% PEG 4000, 100mM Na Citrate, 200mM NH4 Acetate, pH 5.9, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.49	α = 90
b = 48.371	β = 92.36
c = 119.236	γ = 90

Symmetry
Space Group	P 1 21 1

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 210	Rh-coated Si mirror for vertical focusing	2007-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.97700	CHESS	A1

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	1.77	50	97.9	0.183	4.8	3.3		91227

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	1.77	1.83	90.5		0.801		2.8	8368

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 entry 1OIV	1.8	19.95	87258	4367	98.36	0.22	0.218	0.22	0.259	0.26	RANDOM	20.274

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]
0.02		-0.07	0.09		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.248
r_dihedral_angle_4_deg	17.331
r_dihedral_angle_3_deg	13.992
r_dihedral_angle_1_deg	5.563
r_scangle_it	2.6
r_scbond_it	1.707
r_angle_refined_deg	1.342
r_mcangle_it	1.309
r_angle_other_deg	0.977
r_mcbond_it	0.821
r_symmetry_hbond_refined	0.28
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.206
r_nbd_other	0.194
r_symmetry_vdw_other	0.193
r_nbtor_refined	0.171
r_mcbond_other	0.165
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.081
r_nbtor_other	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6620
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	158

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection