2RGI | pdb_00002rgi

Crystal structure of Ca2+-free S100A2 at 1.6 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KSO	MODEL based S100A3 pdb code 1KSO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	293	0.1 M sodium acetate, 10% isopropanol, 35-40% PEG 4000, pH 7.4, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.69965	27.632162

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.516	α = 90
b = 57.82	β = 90
c = 59.794	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	MARMOSAIC 225 mm CCD		2005-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97927	SLS	X06SA

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	1.6		97.7	0.086	14.59			20053		-3	24.443

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)
	1.6	1.8	95.4		0.56	3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	MODEL based S100A3 pdb code 1KSO	1.6	19.28	20053	20053	1003	100	0.188	0.188	0.186	0.2	0.227	0.24	RANDOM	11.88

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.027
r_dihedral_angle_3_deg	15.946
r_dihedral_angle_1_deg	5.858
r_scangle_it	3.801
r_scbond_it	2.314
r_mcangle_it	1.454
r_angle_refined_deg	1.445
r_angle_other_deg	1.393
r_mcbond_it	0.832
r_nbd_refined	0.247
r_mcbond_other	0.233
r_symmetry_vdw_refined	0.219
r_symmetry_vdw_other	0.21
r_symmetry_hbond_refined	0.199
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.178
r_nbd_other	0.175
r_metal_ion_refined	0.135
r_nbtor_other	0.093
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_symmetry_metal_ion_refined	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1476
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	3

Software

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