3MJH | pdb_00003mjh

Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.412	α = 90
b = 80.398	β = 90
c = 103.495	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2007-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	50	97.1	0.042	44.7	4.5		27931		-3	35.344

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.03	20	21886	21886	1157	89	0.195	0.19568	0.19229	0.2073	0.25989	0.2045	RANDOM	37.193

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]
2.53			-1.26		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.652
r_dihedral_angle_3_deg	15.684
r_dihedral_angle_4_deg	13.815
r_dihedral_angle_1_deg	5.839
r_scangle_it	2.213
r_scbond_it	1.417
r_angle_refined_deg	1.203
r_mcangle_it	1.037
r_mcbond_it	0.608
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.218
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.122
r_metal_ion_refined	0.091
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3138
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	68

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling