3HP3 | pdb_00003hp3

Crystal structure of CXCL12

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		300	0.1 M Tris-HCl pH 8.5, 20% Jeffamine M-600, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.834	α = 90
b = 117.468	β = 90
c = 134.501	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r			M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0400	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	31					39406

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	29.18	33679	709	99.63	0.2294	0.22832	0.2388	0.27995	0.2879	RANDOM	28.569

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]
-0.57			0.03		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.218
r_dihedral_angle_3_deg	19.248
r_dihedral_angle_4_deg	16.225
r_scangle_it	10.726
r_scbond_it	8.485
r_mcangle_it	8.245
r_mcbond_it	6.287
r_dihedral_angle_1_deg	6.086
r_angle_refined_deg	1.229
r_chiral_restr	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4979
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CBASS	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling