8CGC | pdb_00008cgc

Structure of CSF1R in complex with a pyrollopyrimidine (compound 23)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I1M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.3 M DL-Malic acid pH 7.0, 23.0% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.013	α = 90
b = 81.013	β = 90
c = 143.237	γ = 120

Symmetry
Space Group	H 3

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 6M		2018-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.99187	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.925	31.895	97.6	0.061	0.071	0.036	0.997	10.7	3.6		25909			28.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.925	1.994	98.2		0.451	0.536	0.282	0.89	2.6	3.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	2i1m	1.925	31.895	25909	1231	97.56	0.154	0.1516	0.16	0.2059	0.21	32.398

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]
-1.17	-0.585		-1.17		3.797

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.568
r_dihedral_angle_3_deg	15.022
r_lrange_it	9.311
r_lrange_other	9.188
r_dihedral_angle_2_deg	8.115
r_dihedral_angle_1_deg	6.86
r_scangle_it	6.507
r_scangle_other	6.506
r_mcangle_other	5.164
r_mcangle_it	5.163
r_scbond_it	4.023
r_scbond_other	4.021
r_mcbond_it	3.364
r_mcbond_other	3.364
r_angle_refined_deg	1.38
r_angle_other_deg	0.495
r_symmetry_nbd_refined	0.265
r_nbd_refined	0.221
r_nbd_other	0.208
r_xyhbond_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.186
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2462
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
REFMAC	phasing