3HD6 | pdb_00003hd6

Crystal Structure of the Human Rhesus Glycoprotein RhCG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B9W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.1M Tris pH 8.5 (at 293K), 40% PEG 200 + 20mM Tris pH 7.4 (at 293K), 100mM NaCl, 40mM BOG, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.83	α = 90
b = 99.83	β = 90
c = 101.076	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 4		2008-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	86.39	99.7	0.077	0.089	39.7	10.6	33464	33449		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	95.8		0.589	0.637	3.4	8.6

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 (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	3B9W	2.1	86.39	33464	31746	1695	99.68	0.16973	0.16837	0.18	0.19505	0.2	RANDOM	24.109

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]
0.69	0.34		0.69		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.159
r_dihedral_angle_3_deg	12.602
r_dihedral_angle_4_deg	9.676
r_dihedral_angle_1_deg	5.133
r_scangle_it	1.881
r_scbond_it	1.204
r_angle_refined_deg	1.018
r_angle_other_deg	0.87
r_mcangle_it	0.79
r_mcbond_it	0.429
r_mcbond_other	0.095
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3163
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	20

Software

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