1XK4 | pdb_00001xk4

Crystal structure of human calprotectin(S100A8/S100A9)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MR8	1MR8 and 1IRJ
experimental model	PDB	1IRJ	1MR8 and 1IRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	285	32% MPD, 0.1M Citrate (pH= 4.2), 20mM Tris (pH= 8.0), 2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.4	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.509	α = 90
b = 78.697	β = 94.94
c = 177.411	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH		2003-11-15	M	SINGLE WAVELENGTH
2	1	100	IMAGE PLATE	MARRESEARCH		2004-07-28

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97960	SLS	X06SA
2	SYNCHROTRON	BESSY BEAMLINE 14.2	0.92000	BESSY	14.2

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	1.8	30	81.03	0.119	3.8005	6.2	102635	99507	6	6

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	1.8	1.9	69.88		0.48	1.44	6.1	12460

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MR8 and 1IRJ	1.8	30	-3	99802	94798	5004	81.02	0.1602	0.15781	0.16	0.20475	RANDOM	27.208

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]
2.25		-1.05	-1.59		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.494
r_dihedral_angle_3_deg	16.05
r_dihedral_angle_4_deg	14.033
r_dihedral_angle_1_deg	5.481
r_scangle_it	3.808
r_mcangle_it	2.93
r_scbond_it	2.494
r_mcbond_it	2.05
r_angle_refined_deg	1.458
r_symmetry_vdw_refined	0.372
r_nbtor_refined	0.315
r_xyhbond_nbd_refined	0.255
r_symmetry_hbond_refined	0.254
r_nbd_refined	0.225
r_metal_ion_refined	0.118
r_chiral_restr	0.115
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_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	8880
Nucleic Acid Atoms
Solvent Atoms	1059
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing