6A8D | pdb_00006a8d

Crystal Structure of Chlamydomonas reinhardtii ARF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HUR	1HUR, 1RRG, 3AQ4, 5A1U
experimental model	PDB	1RRG	1HUR, 1RRG, 3AQ4, 5A1U
experimental model	PDB	3AQ4	1HUR, 1RRG, 3AQ4, 5A1U
experimental model	PDB	5A1U	1HUR, 1RRG, 3AQ4, 5A1U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	20% PEG8000, 200mM Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.818	α = 90
b = 44.244	β = 90
c = 113.481	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	100	IMAGE PLATE	RIGAKU RAXIS IV++		2016-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	Cu FINE FOCUS	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.34	56.75	98.8	0.1	0.029	35.71	10.7		9681

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	92.8		0.734	0.259	0.887	2.44	5.9

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	1HUR, 1RRG, 3AQ4, 5A1U	2.34	56.74	9171	448	98.47	0.22251	0.22037	0.22	0.26563	0.27	RANDOM	57.58

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]
-0.49			4.48		-3.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.664
r_dihedral_angle_3_deg	22.19
r_dihedral_angle_4_deg	17.912
r_long_range_B_other	9.737
r_long_range_B_refined	9.734
r_dihedral_angle_1_deg	7.887
r_mcangle_it	7.234
r_mcangle_other	7.23
r_scangle_other	7.109
r_scbond_other	4.857
r_scbond_it	4.851
r_mcbond_other	4.793
r_mcbond_it	4.792
r_angle_refined_deg	1.991
r_angle_other_deg	1.134
r_chiral_restr	0.129
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1410
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing