6QMT

Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	25% PEGME 3350, 100 mM Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.964	α = 83.03
b = 39.235	β = 75.34
c = 63.502	γ = 65.17

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	DECTRIS PILATUS 2M		2012-01-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.63	61.41	92.9	0.05	0.063	10.93	2.35		37403	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.73	84.3		0.31	0.4	2.49	2.15

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1DSU	1.8	35.6	26852	1414	94.82	0.2035	0.202	0.2312	RANDOM	25.871

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]
-0.02	0.04	-0.03	0.13	0.06	-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.838
r_dihedral_angle_4_deg	19.976
r_dihedral_angle_3_deg	19.052
r_mcangle_it	4.283
r_mcbond_it	3.47
r_dihedral_angle_1_deg	3.391
r_mcbond_other	3.283
r_angle_other_deg	2.496
r_angle_refined_deg	1.921
r_chiral_restr	0.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.838
r_dihedral_angle_4_deg	19.976
r_dihedral_angle_3_deg	19.052
r_mcangle_it	4.283
r_mcbond_it	3.47
r_dihedral_angle_1_deg	3.391
r_mcbond_other	3.283
r_angle_other_deg	2.496
r_angle_refined_deg	1.921
r_chiral_restr	0.146
r_bond_other_d	0.035
r_bond_refined_d	0.016
r_gen_planes_other	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3362
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.