2D9Q | pdb_00002d9q

Crystal Structure of the Human GCSF-Receptor Signaling Complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CD9	PDB ENTRY 1CD9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	0.2M ammonium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.17	76.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.777	α = 90
b = 134.777	β = 90
c = 105.468	γ = 120

Symmetry
Space Group	P 32 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 QUANTUM 4		2003-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

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	2.8	50	91	0.058	20.3	5.9		25214			43.4

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	2.8	2.9	78		0.355	1.9	2.2	2129

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	MIR and MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1CD9	2.8	20	23837	23837	1264	91.21	0.25311	0.25311	0.25145	0.24	0.28445	0.28	RANDOM	68.031

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]
3.32	1.66		3.32		-4.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.748
r_mcangle_it	3.667
r_scangle_it	3.209
r_angle_refined_deg	2.975
r_mcbond_it	2.089
r_scbond_it	1.878
r_angle_other_deg	1.182
r_symmetry_vdw_refined	0.35
r_symmetry_hbond_refined	0.347
r_nbd_refined	0.314
r_symmetry_vdw_other	0.308
r_nbd_other	0.296
r_xyhbond_nbd_refined	0.241
r_chiral_restr	0.143
r_nbtor_other	0.126
r_bond_refined_d	0.037
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3605
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
SHARP	phasing
PHASER	phasing