4HMM | pdb_00004hmm

Crystal structure of mutant rabbit PRP 121-230 (S174N)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O79	PDB ENTRY 3O79

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	100mM SODIUM CACODYLATE PH 6.5, 3.0M NACL, 30% GLYCEROL (cryoprotectant), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.59	α = 90
b = 86.25	β = 90
c = 87.08	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 300 mm CCD		2008-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9793	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.5	60	99.8	0.116	0.097	17.59	4.6	36582	36582

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.6	99.9		0.46	0.595	4.64	4.8	6321

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 3O79	1.5	61.28	36582	34756	1826	99.79	0.14961	0.14716	0.15	0.19318	0.2	RANDOM	15.803

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]
-0.59			-0.47		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.05
r_sphericity_free	23.305
r_dihedral_angle_4_deg	17.839
r_sphericity_bonded	13.669
r_dihedral_angle_3_deg	13.596
r_dihedral_angle_1_deg	6.389
r_rigid_bond_restr	5.63
r_angle_other_deg	1.622
r_angle_refined_deg	1.532
r_chiral_restr	0.096
r_gen_planes_other	0.023
r_gen_planes_refined	0.02
r_bond_refined_d	0.016
r_bond_other_d	0.007
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1686
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling