1ZGX | pdb_00001zgx

Crystal structure of ribonuclease mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RGG	PDB entry 1rgg

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	ammonium sulfate, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	37.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.582	α = 90
b = 41.513	β = 90
c = 58.403	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	AREA DETECTOR	MARRESEARCH	mirrors	2003-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	1.096	EMBL/DESY, HAMBURG	X31

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	1.12	33.9	97.2	0.053	31	5.3	32158				11.5

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)
	1.12	1.13	85		0.306	2.7	2.3	497

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 (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	PDB entry 1rgg	1.13	33.9	32156	29977	1595	98.01	0.12942	0.12754	0.13	0.16395	0.16	RANDOM	9.273

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]
0.16			-0.05		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.9
r_sphericity_free	6.256
r_sphericity_bonded	4.086
r_scangle_it	3.746
r_scbond_it	2.931
r_mcangle_it	2.471
r_angle_other_deg	2.19
r_angle_refined_deg	2.103
r_mcbond_it	1.774
r_rigid_bond_restr	1.611
r_symmetry_vdw_other	0.337
r_nbd_refined	0.309
r_nbd_other	0.251
r_xyhbond_nbd_refined	0.24
r_symmetry_vdw_refined	0.235
r_symmetry_hbond_refined	0.206
r_chiral_restr	0.16
r_nbtor_other	0.087
r_bond_refined_d	0.032
r_gen_planes_other	0.029
r_gen_planes_refined	0.016
r_bond_other_d	0.004
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	759
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing