1NA8 | pdb_00001na8

Crystal structure of ADP-ribosylation factor binding protein GGA1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	289	sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.52	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.426	α = 90
b = 65.426	β = 90
c = 142.725	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	MARRESEARCH		2001-12-20	M	SINGLE WAVELENGTH

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

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	2.3	57	99	0.053	23.7	5.6		16193	5.9	-3	45

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	2.3	2.36	99		0.306	5.9	5.7

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 (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	PDB ID 1GYU	2.3	15	15310	813	98.93	0.21869	0.21869	0.21571	0.22	0.27923	0.28	RANDOM	23.119

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]
1.92	0.96		1.92		-2.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.167
r_scangle_it	3.992
r_dihedral_angle_1_deg	3.689
r_scbond_it	2.31
r_angle_refined_deg	1.718
r_mcangle_it	1.483
r_mcbond_it	0.803
r_angle_other_deg	0.802
r_symmetry_hbond_refined	0.563
r_symmetry_vdw_refined	0.269
r_symmetry_vdw_other	0.264
r_nbd_refined	0.239
r_nbd_other	0.236
r_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_other	0.106
r_chiral_restr	0.091
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_nbtor_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2327
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CNS	refinement
CCP4	data scaling