4NIP | pdb_00004nip

GVIGIAQ segment 147-153 from Human Superoxide Dismutase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	1 M sodium acetate pH 4.5, 1.75 M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.65	25.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.128	α = 90
b = 4.843	β = 99.5
c = 18.142	γ = 90

Symmetry
Space Group	C 1 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	MAR CCD 165 mm		2007-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.895432	ESRF	ID13

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	1.9	90	95.2	0.144	8.5	2.4	415	415		-3	20.8

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	1.9	2.05	89.2		0.206		2.4	74

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	24.85	378	378	43	96.12	0.2339	0.2321	0.24	0.2485	0.27	RANDOM	17.1302

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]
2.35		-0.74	-2.33		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.609
r_mcbond_it	6.377
r_mcangle_it	5.949
r_scbond_it	4.287
r_dihedral_angle_1_deg	3.286
r_scangle_it	3.158
r_mcbond_other	2.278
r_angle_refined_deg	1.316
r_angle_other_deg	0.734
r_dihedral_angle_2_deg	0.639
r_symmetry_vdw_other	0.213
r_xyhbond_nbd_refined	0.198
r_nbd_other	0.186
r_nbtor_refined	0.142
r_chiral_restr	0.09
r_nbd_refined	0.085
r_nbtor_other	0.068
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	46
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction