5FCR | pdb_00005fcr

MOUSE COMPLEMENT FACTOR D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FCK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Mouse FD was crystallized by the sitting drop vapour diffusion method. A 1 uL FD solution (14.4 mg/mL FD, 50 mM Tris pH 8.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0) and equilibrated against 200 uL reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.271	α = 90.46
b = 52.866	β = 98.04
c = 84.278	γ = 90.14

Symmetry
Space Group	P 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	PIXEL	PSI PILATUS 6M		2010-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

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	1.25	88.35	88.3	0.04	13.9	1.8		215515

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	1.25	1.28	75.1		0.72		1.7

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 (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	5FCK	1.25	83.45	204735	10776	88.27	0.15209	0.14979	0.16	0.19599	0.2	RANDOM	17.735

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	-0.31		-0.14	-0.08	0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	33.992
r_dihedral_angle_2_deg	33.494
r_sphericity_bonded	21.176
r_dihedral_angle_4_deg	19.145
r_dihedral_angle_3_deg	12.587
r_long_range_B_refined	7.877
r_long_range_B_other	7.877
r_scangle_other	7.62
r_scbond_it	7
r_scbond_other	6.996
r_rigid_bond_restr	6.679
r_dihedral_angle_1_deg	6.37
r_mcangle_it	5.448
r_mcangle_other	5.448
r_mcbond_it	4.43
r_mcbond_other	4.427
r_angle_refined_deg	2.7
r_angle_other_deg	2.304
r_chiral_restr	0.185
r_bond_refined_d	0.032
r_bond_other_d	0.018
r_gen_planes_refined	0.017
r_gen_planes_other	0.011
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6947
Nucleic Acid Atoms
Solvent Atoms	840
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing