1PK6 | pdb_00001pk6

Globular Head of the Complement System Protein C1q

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GR3	PDB: 1GR3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 4000, CaCl2, B-mercaptoethanol, agarose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.182	α = 90
b = 53.222	β = 112.32
c = 90.88	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC		1998-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0	ESRF	ID29

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	1.85	25.4	90	0.073	7.1	4.73	26237	26090

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)
	1.86	1.98	67.2		0.23	1.7	1.1

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 (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: 1GR3	1.85	25.4	26237	21245	1074	85.09	0.20057	0.20057	0.19869	0.21	0.23858	0.24	RANDOM	24.877

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]
		0.03	-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.06
r_scangle_it	3.428
r_angle_other_deg	2.611
r_scbond_it	1.925
r_mcangle_it	1.823
r_angle_refined_deg	1.321
r_mcbond_it	0.96
r_symmetry_vdw_other	0.338
r_nbd_other	0.274
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.181
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.144
r_nbtor_other	0.105
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_dihedral_angle_2_deg
r_xyhbond_nbd_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	3115
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
AMoRE	phasing